Customs and Import/Export Compliance for E-Commerce in Lithuania

AT A GLANCE

Goods imported into the EU from non-EU countries are generally subject to customs declarations and applicable import taxes. However, customs duties and import VAT are not universally payable on every shipment. Exemptions and special customs procedures may apply depending on the goods, their value, origin and intended use. Since 1 July 2026, the EU has applied a temporary EUR 3 customs duty to qualifying low-value consignments not exceeding EUR 150, calculated for each distinct tariff classification represented in a consignment. Import VAT generally applies unless a specific exemption is available, including qualifying imports under the IOSS scheme.
Incorrect HS code classification is one of the most common and most expensive e-commerce customs errors — resulting in underpaid duties discovered on audit, with backdated assessments plus penalties.
IOSS (Import One Stop Shop) allows e-commerce sellers to collect VAT at the point of sale on low-value goods (below €150) imported from non-EU countries, eliminating border VAT charges that generate consumer complaints and returns.
Lithuania is a full EU customs union member — goods imported into Lithuania are in free circulation across all 27 EU member states; goods exported from Lithuania to non-EU countries leave the EU customs territory.
We provide customs advisory, HS code classification, IOSS registration, origin documentation, and Intrastat reporting support — advising before the first shipment, not after the first customs hold.

Customs and import/export compliance for an e-commerce business covers the obligations that arise when physical goods cross international borders — importing products from non-EU suppliers into Lithuania, selling goods to customers outside the EU, or moving goods between EU member states. The key areas are: customs duty calculation based on the correct HS commodity code and country of origin; import VAT management and reclaim; IOSS registration and monthly returns for low-value imports to EU consumers; country of origin documentation for preferential duty rates under EU trade agreements; and Intrastat statistical reporting for intra-EU goods movements. We advise on all of these before shipments begin, preventing the unexpected costs and delays that arise when customs compliance is treated as an afterthought.

How the EU Customs Framework Applies to E-Commerce

Lithuania is part of the EU customs union — a single customs territory in which goods move freely once they have cleared customs at the point of entry. A shipment imported into Lithuania from China clears EU customs at the Lithuanian border and is then in free circulation across all 27 member states. Conversely, goods exported from Lithuania to a non-EU country leave the EU customs territory and are subject to the import requirements of the destination country.

For e-commerce businesses, the customs framework creates obligations at four distinct points: when goods are imported into the EU (customs duties and import VAT); when goods are sold to non-EU consumers (export documentation and destination country import compliance); when low-value goods are sold to EU consumers from non-EU warehouses (IOSS); and when goods move between EU member states above statistical thresholds (Intrastat).

Why customs compliance matters for e-commerce

The cost implications of getting customs wrong are not hypothetical — they arrive as bills. A company that has been importing goods under an incorrect HS code, and therefore paying too little duty, receives a backdated assessment covering every import in the relevant period plus interest and penalties. A company that has been importing goods under an HS code for which a preferential duty rate was available — but not claimed, because the origin documentation was not in place — has been overpaying duty on every shipment. For an e-commerce business importing several containers per year, both errors represent thousands of euros of unnecessary cost.

The three-layer cost of importing goods into the EU

Importing goods into Lithuania may involve customs duties, import VAT and customs clearance costs. Customs duties depend on the applicable EU tariff classification, origin, customs value and any preferential arrangements or exemptions. From 1 July 2026, a temporary EUR 3 customs duty applies to qualifying low-value consignments under the relevant EU rules. Lithuanian import VAT is generally calculated using the applicable VAT rate on a taxable amount that includes the customs value, relevant customs duties and certain additional costs, including qualifying transport and insurance expenses. Depending on the importer’s VAT status and applicable procedures, import VAT may be accounted for through the VAT return rather than paid directly at customs clearance. Customs broker fees arise where a broker is engaged and are not universally mandatory. We advise on all three costs at the product and supplier level before the first shipment arrives.

De minimis threshold abolished

The EU abolished the EUR 22 import VAT exemption on 1 July 2021. Import VAT generally applies to commercial imports regardless of value, subject to statutory exemptions and special procedures. The Import One Stop Shop (IOSS) provides an optional mechanism for collecting and declaring VAT on qualifying distance sales of imported goods in consignments with an intrinsic value not exceeding EUR 150, excluding excise goods. From 1 July 2026, the EU also introduced a temporary EUR 3 customs duty on qualifying low-value consignments, replacing the previous general customs duty exemption for such consignments within the scope of the measure. Use of IOSS does not eliminate applicable customs duties or customs declaration requirements. The abolition of the de minimis threshold significantly increased the compliance burden for e-commerce businesses shipping small parcels from non-EU warehouses.

Our Customs and Trade Compliance Services

We provide customs advisory across five areas — covering the planning, documentation, and reporting obligations that apply to e-commerce businesses importing and exporting physical goods.

HS Code Classification and Customs Duty Advice

The Harmonised System (HS) commodity code is the foundation of customs compliance — it determines the customs duty rate, import VAT treatment, any applicable trade remedy duties (anti-dumping, countervailing), and the export licensing requirements. For an e-commerce business importing a range of products, the HS code for each product must be correctly determined before the first import. A customs agent will file whatever code they are told — correct classification is the importer's legal responsibility.

HS code classification advice for specific products — identifying the correct 8-digit EU combined nomenclature code
Customs duty rate confirmation — the applicable standard duty rate and any preferential rates under EU trade agreements
Anti-dumping and countervailing duty assessment — confirming whether trade remedy duties apply to specific product-country combinations
Customs classification opinion — written opinion on the correct HS code for a specific product, with supporting rationale
Classification review for existing product ranges — reviewing current HS codes against the actual product descriptions
Binding Tariff Information (BTI) application support — assisting with applications for official classification rulings from Lithuanian Customs
Classification update monitoring — tracking EU customs tariff changes that affect existing HS code assignments

Anti-dumping duties

Several product categories imported from China carry anti-dumping duties in addition to standard customs duties. Common e-commerce product categories affected include: certain ceramics, solar panels, steel products, bicycles, some fasteners, and specific chemical products. Anti-dumping duties can range from a few percent to over 50% of customs value — potentially making a product commercially unviable if not identified before sourcing. We check for applicable trade remedy duties as part of every HS classification engagement.

Import VAT Planning and Reclaim

Import VAT in Lithuania is generally calculated using the applicable VAT rate on the taxable amount determined under Lithuanian VAT legislation. This amount may include the customs value, customs duties and other qualifying incidental expenses. The standard Lithuanian VAT rate is 21%, although reduced rates and exemptions may apply to certain goods. Lithuanian VAT-registered businesses may deduct import VAT to the extent that the imported goods are used for activities giving rise to input VAT deduction rights and the applicable documentary requirements are satisfied. Import VAT may also be accounted for through the Lithuanian VAT return where the relevant conditions are met. Import VAT is not automatically fully recoverable in every case, nor does the absence of a Lithuanian VAT number necessarily make it a permanent cost in all circumstances.

Import VAT registration advice — whether and when a Lithuanian VAT number is needed for efficient import operations
Importer of record setup — structuring the import so the Lithuanian entity is correctly identified as importer for VAT reclaim purposes
Deferred payment scheme — advising on Lithuanian customs deferred VAT payment mechanisms available to authorised importers
Import VAT reclaim procedure — confirming the documentation required to support input VAT claims on import entries
VAT treatment of imported goods for resale vs. own use — different treatment for goods entering stock vs. goods for internal use
Cross-border triangulation — VAT treatment when goods are shipped from a non-EU supplier directly to an EU customer without physically entering Lithuania
Import VAT on returned goods — procedure for recovering import VAT on goods subsequently returned to the non-EU supplier

IOSS Registration and Returns

The Import One Stop Shop (IOSS) is the EU's scheme for collecting and remitting VAT on goods valued at €150 or less imported from non-EU countries and sold directly to EU consumers. Under IOSS, the seller registers in Lithuania, collects VAT from the consumer at the point of sale at the consumer's country rate, and remits it through a monthly return to VMI. Goods then clear customs without additional VAT charges at the border. Without IOSS, the postal carrier or courier collects VAT from the consumer on delivery — creating friction, consumer complaints, and return rates.

IOSS eligibility assessment — confirming whether your fulfilment model qualifies for IOSS and which sales it covers
IOSS registration with VMI — obtaining the IOSS identification number used on all covered import declarations
Monthly IOSS return preparation and filing — country-level sales data at the correct local VAT rate for all covered transactions
IOSS rate table maintenance — keeping the correct VAT rate for each EU member state current as rates change
IOSS and marketplace interaction — advising on how IOSS interacts with Amazon, eBay, and other marketplaces that may have their own IOSS registration
Non-EU warehouse logistics structure — advising on how to structure the logistics flow for IOSS-eligible shipments
IOSS record-keeping requirements — the transaction records that must be maintained and made available to VMI on request

IOSS and marketplace-facilitated sales

Online marketplaces may be treated as deemed suppliers for qualifying distance sales of imported goods in consignments with an intrinsic value not exceeding EUR 150. Where the marketplace uses IOSS for those transactions, the underlying seller generally does not need a separate IOSS registration for the marketplace-facilitated sales. Sellers making direct sales through their own websites may choose to register for IOSS where eligible, but registration is optional. Without IOSS, import VAT must be handled through the applicable customs and VAT procedures. A marketplace's IOSS identification number must not be used for sales that are not covered by that marketplace's deemed-supplier arrangements. We assess which sales require your own IOSS registration and which are covered by the marketplace.

Country of Origin and Preferential Duty Rates

The country of origin of imported goods determines whether preferential duty rates under EU trade agreements apply — and, in the case of anti-dumping duties, whether additional trade remedy charges are triggered. Many e-commerce businesses overpay customs duties because they do not claim the preferential rates available under the EU's trade agreements with specific countries. Others unknowingly misrepresent the origin of their goods, creating customs fraud exposure. We advise on origin rules and the documentation required to support preferential duty claims.

Rules of origin analysis — confirming the country of origin for goods that are manufactured or processed in multiple countries
EU trade agreement preferential rate identification — identifying applicable preferential duty rates under EU FTAs (EU-UK, EU-Vietnam, EU-South Korea, EU-Japan, and others)
Proof of origin documentation — what documents are required (EUR.1 movement certificate, origin declaration, REX registration) for each trade agreement
Registered Exporter (REX) system advisory — advising non-EU suppliers on REX registration to enable them to certify origin on shipments
General Scheme of Preferences (GSP) — identifying whether goods from developing countries qualify for reduced GSP duties
Origin misrepresentation risk assessment — reviewing current import documentation for incorrect origin declarations
Anti-circumvention assessment — advising on whether goods processed in third countries are at risk of anti-circumvention duty investigations

Export Compliance and Documentation

Exporting goods from Lithuania to non-EU countries requires export documentation, compliance with EU export restrictions, and an understanding of the destination country's import requirements. For e-commerce businesses that ship globally — to the UK, the US, the GCC, or Asian markets — export compliance affects both the cost of selling internationally and the regulatory obligations of the Lithuanian entity as the EU exporter.

Export declaration requirements — when export customs declarations are required and how they are filed in Lithuania
EU export licensing — identifying whether any products are subject to EU export controls or dual-use goods regulations
UK import compliance — assessment of post-Brexit customs obligations, applicable commodity codes, UK EORI registration requirements, import VAT and duty liabilities, and the appropriate customs declaration procedures. The analysis must distinguish Great Britain from Northern Ireland, which is subject to specific arrangements for trade in goods under the Windsor Framework.
US Customs and Border Protection (CBP) requirements — Harmonized Tariff Schedule (HTS) classification, applicable import duties and additional tariffs, importer identification, customs bond requirements, entry procedures and product-specific restrictions. The former Section 321 duty-free de minimis exemption for qualifying shipments valued at USD 800 or less was suspended for covered imports from all countries effective 29 August 2025. US import compliance assessments must therefore reflect the currently applicable customs entry and duty rules rather than assuming that small shipments qualify for duty-free entry.
Destination country import duty research — identifying the applicable import duty rate in the destination country for specific products
Export documentation — commercial invoice content requirements, packing lists, certificates of origin, and export accompanying documents
Incoterms advice — recommending the appropriate delivery terms for international sales and their impact on customs responsibility

Intrastat Statistical Reporting

Intrastat is the system for collecting statistics on the movement of goods between EU member states. Lithuanian companies that move goods into Lithuania from other EU member states (arrivals) or dispatch goods from Lithuania to other EU member states (dispatches) above the annual thresholds must file monthly Intrastat declarations with Lietuvos statistika. While Intrastat is statistical rather than tax-related, late or missed filings attract administrative fines — and the threshold can be reached more quickly than operators expect.

Intrastat threshold monitoring — tracking qualifying intra-EU movements of goods against Lithuania's 2026 reporting thresholds: EUR 600,000 for arrivals and EUR 400,000 for dispatches. These thresholds are assessed separately using the preceding calendar year's relevant trade value or the cumulative value during the current year. Once the applicable threshold is exceeded, monthly Intrastat reporting is generally required beginning with the month in which the threshold is exceeded.
Monthly Intrastat declaration preparation and filing — commodity code, value, quantity, and member state of origin/destination
Intrastat registration with Lietuvos statistika — where threshold is met or expected to be met
Intrastat commodity code mapping — aligning the e-commerce product range to the correct Intrastat codes
Combined nomenclature vs. Intrastat coding — advising where customs HS codes and Intrastat codes diverge
Prior period Intrastat filings — catching up on missed declarations before regulatory review

Illustrative EU Customs Duty Rates by Product Category

The table below shows indicative customs duty rates for common e-commerce product categories imported from China under the EU’s standard (MFN) tariff. Actual rates depend on the specific HS code — there can be significant variation within a product category depending on the material, construction, and end use. Preferential rates may apply under EU trade agreements with specific countries.

Product Category	Indicative MFN Duty Rate	Anti-Dumping Risk	Notes
Consumer electronics (phones, tablets, laptops)	0%	Low	Most electronics: 0% under ITA agreement
Clothing and apparel	12%	Low	Duty applies to most garments; some knitted/woven distinctions
Footwear	3.7–17%	Low	Rate varies by upper material and sole construction
Toys and games	4.7%	Low	Standard rate; safety certification also required
Furniture	2.7–5.6%	Low	Varies by material; Chinese-origin wooden furniture: 8% on some items
Sports and fitness equipment	2.7%	Low	Most sporting goods; bicycles are higher
Bicycles	14.5%	High	Plus anti-dumping duty up to 48.5% on Chinese-origin bikes
Cosmetics and skincare	0–6.5%	Low	Varies by product type; some items exempt
Home and garden items	3–12%	Low	Wide variation by specific product
Ceramics and tableware	12%	Medium	Some Chinese ceramics subject to anti-dumping investigation
Solar panels	0%	High	Historically subject to anti-dumping; currently suspended — monitor
Steel products	Varies	High	Many steel categories subject to safeguard and anti-dumping duties

Rates change — verify before each import
EU customs duty rates can change when new anti-dumping investigations are initiated, when trade agreements enter into force, or when tariff schedule reviews take effect. The rates above are indicative as of the date of this publication. We verify the applicable rate at the time of each classification engagement — not from a static reference table. Importing under an outdated duty rate exposes the company to underpayment liability.

Post-Brexit UK–EU Trade: What Lithuanian E-Commerce Companies Need to Know

The UK left the EU customs union on 31 December 2020. Since then, goods moving between Lithuania and the UK are subject to customs formalities in both directions — they are treated as imports and exports, not as intra-EU movements. For Lithuanian e-commerce companies that source goods from UK suppliers, sell goods to UK consumers, or use UK warehouses, the post-Brexit framework has significant practical implications.

Importing goods from UK suppliers into Lithuania

Goods purchased from UK suppliers and imported into Lithuania are subject to EU import customs duties at the applicable MFN rate — unless preferential treatment is available under the EU-UK Trade and Cooperation Agreement (TCA). Under the TCA, goods that originate in the UK (meeting the product-specific rules of origin) can be imported into the EU at 0% customs duty, provided the correct proof of origin is presented. To claim preferential tariff treatment under the EU-UK Trade and Cooperation Agreement, the importer must have an acceptable basis for demonstrating the originating status of the goods. This may be a statement on origin issued by the UK exporter or the importer’s knowledge supported by appropriate evidence. UK exporters generally use their UK EORI number as the exporter reference on statements on origin. Registration in the EU Registered Exporter (REX) system is not required for UK exporters under this agreement. Goods that do not originate in the UK — for example, Chinese-manufactured goods shipped through a UK warehouse — do not qualify for TCA preferential treatment.

Selling goods to UK consumers

Goods sold to UK consumers from a Lithuanian entity are EU exports and UK imports. The UK’s standard import duty rates apply, plus UK import VAT at 20%. For goods valued below £135 sold to UK consumers through a website, the seller is responsible for collecting and remitting UK VAT at the point of sale — regardless of where the seller is based. Lithuanian e-commerce companies selling to UK consumers at scale may need to register for UK VAT. We advise on UK VAT registration obligations and introduce specialist UK tax advisors where required.

Using UK fulfilment centres

E-commerce businesses that store goods in UK fulfilment centres and dispatch from there to EU consumers are importing goods from the UK into the EU on each shipment — subject to EU customs duties and import VAT unless IOSS applies for sub-€150 consignments. This structure has materially different cost implications from shipping from an EU warehouse. We model the customs duty and import VAT cost of UK-warehoused goods before recommending this fulfilment approach.

Customs Compliance Advisory Pricing

Defined advisory engagements are priced at fixed fees. Complex multi-product classification projects, customs audit defence, and ongoing compliance monitoring programmes are quoted on request based on the scope and volume of work involved.

Service	Price
HS code classification — single product Written opinion with supporting rationale; confirms duty rate and trade remedy check	€150
HS code classification — product range (up to 10 products) Batch classification with duty rate summary table	€800
HS code classification — product range (11–30 products) Includes duty rate optimisation review and anti-dumping assessment	€1,500
HS code classification — full catalogue (30+ products) Quoted based on product complexity and volume	On request
Binding Tariff Information (BTI) application support Preparing the application for a formal Lithuanian Customs classification ruling	€400
Import VAT structure review Assessing whether current import arrangements maximise VAT reclaim efficiency	€350
Importer of record setup advisory Confirming correct structure for Lithuanian VAT reclaim on imports	€300
IOSS registration with VMI Full IOSS registration; IOSS number issued; included in VAT retainer thereafter	€500
Monthly IOSS return preparation and filing For clients on our VAT-registered e-commerce accounting retainer	Included in VAT retainer
IOSS standalone monthly return (no accounting retainer) For clients who handle their own accounting but need IOSS filing support	€150 / month
EU trade agreement preferential rate assessment Identifying applicable preferential rates for a specific supplier and product range	€400
Rules of origin analysis — single product Confirming country of origin and applicable proof of origin requirements	€250
REX supplier advisory Advising a non-EU supplier on Registered Exporter registration to support preferential claims	€200
Export compliance review — UK market Post-Brexit UK import requirements, commodity codes, and EORI setup	€500
Destination country import duty research (per country) Identifying applicable import duty rate and documentation requirements in a target export market	€200
Export documentation review Reviewing commercial invoices, packing lists, and certificates of origin for compliance	€300
Intrastat registration with Lietuvos statistika One-off registration where threshold is met	€150
Monthly Intrastat declaration preparation and filing Per declaration; included in accounting retainer for retainer clients	€100 / month
Customs compliance health check Full review of current import/export practices against EU customs requirements	€800
Ongoing customs advisory retainer Monthly advisory covering classification updates, duty rate changes, and ad hoc queries	On request

Classification fees — a note on cost vs. risk
An HS code classification for a single product costs €150. An underpaid customs duty liability on 24 months of imports of that product — discovered during a Lithuanian Customs audit — is calculated as the underpaid duty on every shipment, plus interest at the applicable rate, plus an administrative penalty. For a company importing a 40-foot container of goods each month, the underpaid duty on a 3% misclassification error accumulates to thousands of euros before the audit finds it. We treat classification advice as risk management, not administration.

Frequently Asked Questions

They are two separate charges applied to goods imported into the EU. Customs duty is a tax on the goods themselves — calculated as a percentage of the customs value (typically the purchase price plus insurance and freight to the EU border). It is payable to Lithuanian Customs at the time of clearance and is not recoverable for VAT-registered businesses. Import VAT is charged at 21% on the customs value plus customs duties — it is also payable at clearance, but a VAT-registered Lithuanian company can reclaim it as input VAT in its monthly Lithuanian VAT return, provided the import is correctly documented with the company’s VAT number as the importer of record. The practical implication: customs duty is always a cost; import VAT is a timing difference for VAT-registered importers.

No. The legal responsibility for correct HS code classification rests with the importer — the Lithuanian company — not with the supplier. The HS code on the supplier’s documentation is the supplier’s classification for export purposes in their own country, which may differ from the EU classification for the same goods. Suppliers also routinely underclassify goods — using codes with lower duty rates — which shifts the liability to the importer if discovered during a customs audit. We recommend independently verifying the correct EU HS code for every product before the first import, and retaining the classification opinion as evidence of due diligence.

IOSS covers goods with a customs value of €150 or less imported from a non-EU country and sold directly to EU consumers by the seller registered for IOSS. It does not apply to: goods with a value above €150 (which require standard customs clearance and import VAT payment at the border); excise goods (tobacco, alcohol) regardless of value; goods subject to special import restrictions; or goods sold through a marketplace that has its own IOSS registration covering those sales. For goods above €150 or outside the IOSS scope, standard customs clearance and import VAT apply — the consumer may be charged at delivery unless the seller handles customs as the importer of record.

Yes, if the goods originate in the UK under the EU-UK Trade and Cooperation Agreement rules of origin. Most goods that are fully produced or sufficiently processed in the UK qualify for 0% customs duty under the TCA. The key is the rules of origin test — goods must meet the product-specific rule for their HS code, which typically requires a minimum percentage of UK content or a transformation of sufficient degree. Preferential treatment under the EU-UK Trade and Cooperation Agreement may be claimed using a valid statement on origin issued by the UK exporter or sufficient supporting information under the importer’s knowledge procedure. UK exporters generally identify themselves using their UK EORI number rather than an EU REX registration. Goods must satisfy the applicable product-specific rules of origin to qualify for preferential treatment. Products manufactured outside the UK and merely stored, repackaged or re-exported from the UK do not acquire UK preferential origin solely because they were shipped from a UK warehouse.

Intrastat is the statistical reporting system for qualifying movements of goods between EU Member States. In Lithuania, the 2026 reporting thresholds are EUR 600,000 for arrivals and EUR 400,000 for dispatches. The thresholds apply to Lithuanian VAT-registered persons and are assessed separately based on relevant goods movements during the preceding calendar year or the cumulative value during the current calendar year. Where a threshold is exceeded during the current year, the corresponding monthly Intrastat declarations must generally be submitted from the month in which the threshold is exceeded. Reporting obligations for the following year depend on the applicable thresholds and relevant trade values. For Amazon FBA sellers with stock in multiple EU fulfilment centres, Intrastat obligations can arise from the stock movements between Amazon warehouses — not just from customer sales.

Most e-commerce goods do not require EU export licences. However, certain categories are subject to EU export controls — primarily dual-use goods (items that have both civilian and military applications), goods subject to EU sanctions against specific countries, and certain military items. Common e-commerce product categories that may trigger export control screening include: drone components, certain electronic equipment, encryption software, and some chemical products. We conduct an export control screening as part of our export compliance review to confirm whether any products in your range require export authorisation before shipment to specific destinations.

A standard commercial export shipment from Lithuania to a non-EU destination generally requires appropriate commercial documentation and an electronic export customs declaration submitted through the applicable customs declaration system. LITAR is Lithuania’s integrated tariff information system and should not be described as the electronic system used to submit export customs declarations. Depending on the goods and destination, additional documents may be necessary, including export licences, certificates of origin, phytosanitary or veterinary certificates and other product-specific authorisations. Phytosanitary certificates generally concern regulated plants and plant products rather than all organic products. CE marking is a product conformity requirement for specified products placed on the relevant market and is not a universal customs export document. For exports to countries with which the EU has a trade agreement, a proof of origin document may be required to support a preferential duty claim at the destination. We review export documentation packages for compliance and identify any missing documents before the shipment departs.

Ready to sort your customs compliance before the next shipment?

Contact us to discuss your product range, supplier countries, and fulfilment model. We will confirm the correct HS codes, identify applicable duty rates and preferential treatments, assess IOSS and Intrastat obligations, and provide fixed-fee quotes for each advisory engagement. Most clients find the first classification engagement pays for itself within a single shipment.

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