EAEU Dossier Alignment after 31 December 2025: Transitional Cases and Portfolio Decisions

The deadline for starting the ordinary procedure of bringing a national medicinal-product dossier into compliance with the Eurasian Economic Union requirements has passed. A new application under Section XIII of the EAEU Rules could be filed in the reference state only up to 31 December 2025.

That does not mean that every national marketing authorization simply became invalid on 1 January 2026. The 2025 amendments to EEC Council Decision No. 78 created transitional mechanisms for procedures that were initiated on time and for certain recognition-state situations that were still incomplete at the end of the transition period.

The regulatory question in 2026 is therefore no longer:

“How do we start dossier alignment?”

It is:

“What exactly was filed before the cut-off, in which state, what stage has the procedure reached, which national authorizations remain legally usable during the transition, and what EAEU dossier must ultimately emerge from that history?”

For a multinational or independent manufacturer with products registered historically in Russia, Kazakhstan, Belarus, Armenia or Kyrgyzstan, this can be surprisingly difficult to reconstruct. The same product may have several national dossiers, different approved specifications and pack texts, an unfinished reference-state alignment procedure, pending recognition states, new variations and an EAEU GMP workstream running in parallel.

Pharegis treats these cases as portfolio-reconstruction and lifecycle-control projects, not as legacy paperwork.

The 31 December 2025 cut-off closed the entry door, not every pending procedure

Section XIII of Decision No. 78 requires medicinal products registered under national rules before the EAEU system to be brought into compliance with the Union requirements through an EAEU procedure.

The key procedural cut-off was 31 December 2025. An application to bring the dossier into compliance had to be submitted to the competent authority or expert organization of the selected reference state by that date.

For products that met that deadline, Decision No. 34 of 22 May 2025 introduced a mechanism allowing national marketing authorizations to remain effective while the EAEU procedure is completed.

For products that did not enter the transition procedure on time, the regulatory position is fundamentally different. The manufacturer no longer has an open-ended right to start Section XIII after the deadline simply because a national authorization or old dossier still exists in an archive or national database.

The first task in any 2026 portfolio review is therefore to separate products into legally different transition states.

Four portfolio scenarios after the cut-off

Scenario 1 — alignment application filed before 31 December 2025 and still pending in the reference state

Where the application was filed in the reference state before the cut-off and the procedure was not completed there by 31 December 2025, Decision No. 34 provides an extension mechanism for the relevant national marketing authorizations.

The extension is linked to the duration of the actual procedure; it is not a new permanent national authorization.

For the states declared in the alignment application, the national authorization can remain effective for the period of the procedure, subject to the limits introduced by the amendment. The reference-state phase is protected for no more than three years from the date of filing in the reference state. The recognition-state phase can receive an additional period of no more than two years from the filing in the recognition state, provided that the recognition-state filing occurs within the applicable three-year reference-state window.

This mechanism is designed to preserve lawful circulation while an on-time EAEU transition is being completed. It is not a reason to leave the procedure dormant.

Scenario 2 — alignment completed in the reference state before the cut-off, but recognition states were still pending

Where the dossier had already been brought into EAEU compliance in the reference state by 31 December 2025 but the procedure was not complete in the declared recognition states, the national authorizations in those recognition states can remain effective for the duration of the recognition work, subject to the applicable transitional limit.

Decision No. 34 allows this protection for no more than two years starting from 31 December 2025 for the declared recognition states.

The regulatory risk here is dossier divergence. The reference state already has an EAEU dossier and assessment history, while the recognition state may still have a national authorization and legacy national product information. Any change introduced during this period has to be controlled against both procedural states.

Scenario 3 — addition of previously registered recognition states was initiated before the cut-off

Decision No. 77 of 12 September 2025 addressed another practical problem: products for which the EAEU transition had progressed, but the holder still needed to add recognition states where the medicinal product had historically been registered under national rules.

The amendment extended the optimized transition logic to applications for variations that identify such recognition states, provided that the relevant procedure was initiated by 31 December 2025.

The EEC explained that this mechanism preserves the validity of the relevant national marketing authorizations during the procedure, but not later than 31 December 2027 in the affected recognition states.

This is a narrow transitional route. It should not be confused with a general right in 2026 to select new national states or reopen national lifecycle procedures.

Scenario 4 — no timely alignment or recognition-state transition was initiated

If no valid transition application was submitted by the cut-off, the product cannot simply be converted into an EAEU product later through the old Section XIII route.

The remaining questions become product- and country-specific:

• whether batches manufactured or imported while the national authorization was valid may continue to be supplied;
• how long those batches may circulate under the applicable transitional and national rules;
• whether a new EAEU registration is commercially justified;
• whether the existing data can support a new EAEU application;
• whether the old national product should be allowed to run out of stock and leave the market.

Decision No. 78 expressly protects circulation of certain legacy stock after expiry or end of the transition, including products already released while the national authorization was valid, subject to the applicable rules and shelf life. But stock continuity is not equivalent to continued authorization of new production under the old regulatory system.

Do not treat “extended national authorization” as a return to the national regulatory model

The 2025 extensions are continuity mechanisms around an EAEU transition procedure.

The final regulatory object is the EAEU dossier, EAEU assessment report, EAEU marketing authorization, EAEU SmPC and patient leaflet, EAEU quality document and the EAEU lifecycle record.

The manufacturer should therefore avoid a common mistake: continuing to manage the product as two independent products—“old Russian product” and “new EAEU product”—when they are in fact two stages of one regulatory history.

Every material action during the transition should be mapped to the future EAEU baseline.

The alignment procedure is not a complete re-registration from zero

Section XIII was designed to convert an existing national registration into the EAEU regulatory framework without pretending that the medicinal product is a newly developed product.

For a product intended to continue circulating in a state where it was already registered, the applicant submits the dossier in CTD structure and provides the required EAEU administrative, quality and supporting documentation.

Decision No. 78 allows historical preclinical and clinical study reports generated before the EAEU framework to be included in Modules 4 and 5 in their available form, without mechanically rewriting every old study report to modern EAEU GLP, GCP or bioequivalence-report formatting standards.

This is important. The procedure is an alignment and expert assessment of the registered product, not a demand to recreate the historical development programme.

At the same time, the existing data still need to be scientifically interpretable and sufficient to support the current product.

The distinction is:

legacy report format may be acceptable; legacy regulatory inconsistency is not.

The main technical work is reconstructing one current dossier from several historical dossiers

The most difficult alignment cases are rarely those with the largest number of documents. They are products that have accumulated different regulatory histories in several EAEU countries.

Examples include:

• different API manufacturers or approved sources;
• different finished-product manufacturing sites;
• different release or shelf-life specifications;
• different analytical procedures;
• different shelf lives;
• different packaging materials or pack sizes;
• different indications, contraindications or dosing language;
• different trade names;
• different variations approved at different dates;
• changes implemented globally but never introduced in every national dossier.

Before the EAEU dossier can be defended, those histories must be reconciled.

Pharegis builds a national-to-EAEU dossier reconciliation matrix showing:

country → currently approved national position → supporting document → proposed EAEU position → discrepancy → regulatory action.

Without that map, the CTD can look complete while silently combining mutually incompatible approved positions.

The reference state becomes the master regulatory history

If the medicinal product was historically registered in more than one member state, the applicant selects one of those states as the EAEU reference state for the alignment procedure.

That selection has long-term consequences.

The reference state performs the main expert assessment and creates the assessment report that will support recognition in the other EAEU states. After alignment, the reference-state dossier becomes the regulatory baseline from which future mutual recognition, variations, confirmation of registration and lifecycle procedures are controlled.

A good transition project therefore does not merely ask which state could process the dossier fastest. It asks which state should reasonably own the future assessment history of the product.

In 2026 that decision may already have been made, but its consequences still need to be managed.

The nominal procedure clock is less important than the unresolved dossier gaps

Section XIII provides a defined expert-review procedure for bringing the dossier into compliance. The formal procedure is not intended to become an indefinite reassessment.

However, requests for missing or clarifying information create applicant clock-stops. Under the Rules, the applicant can receive up to 90 calendar days to provide the requested information during the alignment expertise, and that response period is excluded from the expert-review timeline.

For an old portfolio, the hard part is often obtaining technically defensible answers from manufacturing sites that no longer have the people who prepared the original dossier.

A query about a specification may require retrieval of old validation data. A question about a manufacturing process may reveal a global change that never entered the national dossier. A question about clinical evidence may require reconstruction of an old study programme and reference-product history.

The correct KPI is therefore not “days since filing”. It is number of unresolved regulatory dependencies that can still stop the transition.

CMC alignment is usually the highest-risk workstream

For long-marketed products, Module 3 is often the part of the dossier that has drifted furthest from the legacy national approval.

A serious alignment review should compare:

• API manufacturer and manufacturing process;
• active-substance specifications and analytical procedures;
• impurity profile and reference standards;
• excipient specifications;
• finished-product composition and manufacturing process;
• manufacturing and testing sites;
• in-process controls;
• finished-product release and shelf-life specifications;
• analytical procedures and validation status;
• process validation;
• packaging system;
• storage conditions;
• shelf life;
• stability commitments;
• current EAEU pharmacopoeial expectations.

The objective is not to preserve every historical national detail. It is to establish one technically supportable EAEU quality position and document how the legacy approvals lead to it.

The quality document is where hidden inconsistencies become visible

During alignment, the EAEU quality document is not simply copied from the old Russian normative document or another member-state specification.

It must represent the control strategy that is supported by the current CTD and can be used for post-registration control in the Union.

This frequently exposes inconsistencies between:

• national release specifications;
• global corporate specifications;
• current analytical procedures;
• CTD 3.2.P.5;
• pharmacopoeial requirements;
• actual commercial batch testing.

A “harmonized” specification that cannot be justified scientifically or reproduced operationally creates a future variation and supply problem even if it is accepted during the transition.

Pharegis therefore treats quality-document reconciliation as a CMC decision, not a formatting step.

EAEU GMP can determine whether a technically complete transition remains usable

Dossier alignment and EAEU GMP status are connected.

Decision No. 34 strengthened this link by addressing manufacturing sites that entered the relevant inspection-planning mechanism but still did not obtain the required EAEU GMP confirmation after completion of the registration procedure.

The current framework allows regulatory consequences where a required manufacturing site remains without valid EAEU GMP evidence after the applicable period.

For an old portfolio, GMP review should therefore ask:

• which manufacturing sites appear in the final EAEU dossier;
• what operations each site performs;
• whether the EAEU GMP scope covers those operations;
• whether an inspection is pending;
• whether the product or site changed during alignment;
• whether the final EAEU dossier and the inspection scope still match.

A dossier brought into compliance on paper but dependent on an unresolved GMP site is not yet a stable regulatory position.

Variations can continue during the transition—but sequencing has to be explicit

The 2025 amendments recognized a practical fact: a medicinal product cannot stop evolving while an alignment or recognition procedure is pending.

Decision No. 78 allows changes to be submitted within the EAEU framework during and after the reference-state alignment process, including before or during completion of recognition-state procedures in the situations described by the amended Rules.

The regulatory team therefore has to maintain at least three dossier baselines:

legacy national approved dossier

EAEU dossier currently under alignment / recognition

next EAEU dossier sequence containing newly approved variations

If those baselines are not controlled, a variation approved in the reference state can disappear from the package used in a recognition state, or a recognition state can complete its procedure against an outdated assessment report.

Pharegis uses a procedure-sequence map to show exactly which variation belongs to which dossier version and when it must propagate to each state.

A narrow national exception should not be mistaken for a general national-variation pathway

The general transition rule established that national confirmation and national medicinal-product dossier variations were available only through 31 December 2025.

At the same time, Decision No. 34 created specific protection for products with timely filed alignment applications and linked the continued validity of national authorizations to those pending procedures. The 2025 amendments also contain narrowly framed mechanisms for managing national records during this transition.

The practical point is not to rely on a blanket statement such as “all national variations ended” or “national variations remain possible”.

For a product still in transition, the correct answer depends on:

• whether a valid Section XIII application was filed before the cut-off;
• which states were declared;
• whether alignment was completed in the reference state;
• whether a recognition-state procedure is pending;
• whether a specific pre-cut-off application to add a recognition state was initiated;
• what the national authority records as the current status of the marketing authorization.

This is one of the areas where a portfolio-level status memo is more useful than a generic rule copied from a presentation.

Product information has to converge, not merely be translated

Old national SmPCs and patient leaflets often differ materially among EAEU states.

Alignment requires more than producing one Russian-language text and translating it.

The EAEU product-information package should reconcile:

• indications;
• dosing;
• contraindications;
• warnings and precautions;
• adverse reactions;
• pregnancy/lactation information;
• pharmacological properties;
• storage conditions;
• pack configuration;
• legal status and local administrative elements.

The scientific core should become one EAEU position, while member-state language and administrative requirements are implemented around that common core.

In 2025 the EAEU also revised the requirements for SmPC and patient information leaflets, including simplifications relevant to previously registered products. A transition dossier prepared several years earlier should therefore be checked against the current requirements before final approval.

Existing stock and packaging need a separate transition plan

Regulatory completion does not mean that every warehouse unit produced under the national authorization must disappear overnight.

Decision No. 78 contains explicit transitional provisions allowing medicinal products released under the national authorization during the transition to continue circulating under the applicable conditions until the end of their shelf life. It also permits coexistence of previously and newly approved packaging and patient information in defined transition situations.

This is important for supply continuity.

The manufacturer should map:

• last batch manufactured under the national dossier;
• last batch released/imported under the national authorization;
• first batch under the EAEU dossier;
• date of EAEU packaging implementation;
• national and EAEU stock by country;
• shelf life of legacy stock;
• labeling/serialization implications;
• any variation that affects the transition batch.

The final regulatory strategy should allow the commercial organization to answer a simple question for every batch: under which authorization and dossier configuration may this batch be released and sold?

Completing the reference-state procedure is not always the end

After a positive reference-state alignment decision, the product may still require recognition in one or more EAEU states.

For states where the product was historically registered, the transition mechanism and declared recognition-state sequence determine how the old national authorization is replaced by the EAEU authorization.

For a member state where the product was not historically registered under the qualifying national framework, the situation is different. Decision No. 78 provides for subsequent mutual-recognition registration after the dossier has been brought into EAEU compliance, and a broader dossier package may be required for that market expansion.

This distinction matters commercially.

Replacing an old national authorization with the EAEU authorization and entering a genuinely new EAEU market are not the same procedure even if they occur around the same time.

Marketing-authorization duration after successful alignment

A successful alignment can also change the future renewal model of the product.

Under Decision No. 78, a medicinal product that has been registered for at least five years in at least three member states can receive an indefinite EAEU marketing authorization through the alignment procedure.

Where that condition is not met, the reference state can issue a five-year authorization requiring subsequent confirmation of registration, with the recognition states following the reference-state term.

For a mature multinational portfolio this is not an administrative detail. It determines whether a further renewal/confirmation project has to be placed on the lifecycle calendar.

When a transition procedure fails

Decision No. 78 allows refusal where the expert assessment does not confirm the quality of the medicinal product or, in the cases requiring such reassessment, where the benefit-risk position is unacceptable.

Failure can also occur procedurally if required information is not supplied within the permitted response period.

For an old national product, refusal has consequences beyond one regulatory submission. The manufacturer can lose the bridge that preserves the national authorization during the transition.

A refusal-response plan should therefore answer in advance:

• can the deficiency be resolved within the active procedure;
• does the response require a CMC variation;
• is additional analytical or stability work needed;
• is a new EAEU registration commercially realistic if alignment ultimately fails;
• how much compliant stock remains in the market;
• what supply or discontinuation communication is required.

Portfolio triage: not every legacy product deserves the same investment

By 2026, dossier alignment should also be a portfolio decision.

A mature product with low revenue, obsolete manufacturing, weak analytical documentation and a site approaching EAEU GMP reinspection may not justify the same remediation investment as a strategically important product intended for several EAEU markets.

Pharegis classifies legacy products into practical groups:

Complete and stabilize

Products with a valid pending transition, strong commercial value and manageable dossier gaps. Priority is to close the EAEU procedure and create a maintainable lifecycle baseline.

Complete and expand

Products with a strong reference-state EAEU dossier and clear commercial value in additional recognition states. Priority is recognition-state sequencing and harmonized implementation.

Remediate before completion

Products where the transition is valid but material CMC, GMP, product-information or evidence gaps could still cause refusal or an unstable approval.

Controlled exit

Products without a viable transition route, insufficient commercial value or an unrepairable dossier/manufacturing position. Priority is lawful stock run-out and market discontinuation rather than regulatory sunk cost.

This portfolio discipline is often more valuable than trying to “save” every historical registration.

What Pharegis manages in a post-2025 EAEU transition project

Pharegis can take over a single stalled procedure or reconstruct an entire legacy portfolio. Typical deliverables include:

• transition-status memo for each product and member state;
• verification of the pre-31 December 2025 filing and applicable extension mechanism;
• reference-state / recognition-state procedure map;
• national-to-EAEU dossier reconciliation matrix;
• CTD completeness and sequence review;
• CMC gap assessment and quality-document reconciliation;
• product-information harmonization;
• EAEU GMP dependency assessment;
• expert-query response strategy;
• variation sequencing during alignment and recognition;
• assessment of recognition-state additions initiated before the cut-off;
• stock, packaging and supply-transition map;
• identification of products suitable for new-market mutual recognition after alignment;
• post-alignment lifecycle plan covering variations, recognition states, GMP and confirmation of registration;
• portfolio recommendation: complete, remediate, expand or discontinue.

For international regulatory teams, the value is not in explaining that the deadline was 31 December 2025. That is already history.

The value is in reconstructing what the company legally preserved before the deadline and converting that procedural history into a single EAEU dossier that can still be operated in 2026 and beyond.

Discuss a pending EAEU dossier-alignment case

For an initial assessment, prepare:

• national marketing-authorization numbers and validity status by EAEU state;
• evidence of the Section XIII application and filing date in the reference state;
• list of recognition states declared in the application;
• current status of the reference-state procedure;
• any recognition-state filings and dates;
• any pre-31 December 2025 application to add recognition states;
• current CTD sequence submitted to the reference state;
• latest national approved dossiers and product information;
• open expert questions;
• manufacturing-site and EAEU GMP status;
• variations filed or approved during the transition;
• current stock and packaging status by country.

Pharegis can then determine which transitional protection applies, which authorization remains operative in each state, what dossier sequence should be treated as authoritative, and what must happen next to reach a stable EAEU lifecycle position.

After 31 December 2025, dossier alignment is no longer a filing opportunity. It is a controlled completion problem—and the value lies in preserving the regulatory position that was secured before the cut-off.

Regulatory basis

• EEC Council Decision No. 78 of 3 November 2016 — Rules for Marketing Authorization and Expert Examination of Medicinal Products for Human Use, including Section XIII on bringing legacy national dossiers into compliance with EAEU requirements.
• EEC Council Decision No. 34 of 22 May 2025 — amendments introducing optimized transition procedures and extension mechanisms for national marketing authorizations while timely filed EAEU procedures are completed.
• EEC Council Decision No. 77 of 12 September 2025 — amendments extending the transition mechanisms to certain pre-cut-off variation procedures used to add recognition states where the medicinal product had previously been nationally registered.
• EEC Council Decision No. 93 of 26 November 2025 — subsequent amendments to the Rules effective from 26 December 2025.
• EEC Council Decision No. 77 of 3 November 2016 — EAEU Good Manufacturing Practice Rules, where manufacturing-site compliance is relevant to the transitioned dossier.

Regulatory status reviewed: August 2026.