Food enzymes from GMO strains under EFSA scrutiny
A wave of new scientific opinions and hard consequences for food manufacturers

Regulation (EC) No 1332/2008 of the European Parliament and of the Council of 16 December 2008 established the EU list of authorised food enzymes — a list that has, to this day, not been published in its final form and remains in the process of being established. It is precisely in this regulatory gap that the risk for manufacturers lies. EFSA, acting on mandates from the European Commission, is assessing successive applications for inclusion on that list, and in doing so is scrutinising ever more closely whether the microorganism strain used to produce the enzyme meets the requirements applicable to GMOs — regardless of whether the final enzyme product contains any detectable GM material.

The regulatory framework: Regulation 1332/2008 and the still-absent EU list

Regulation (EC) No 1332/2008 introduced a harmonised authorisation system for food enzymes at EU level. Under Article 4(1), only enzymes included on the EU list may be placed on the market as such or used in food. The transitional provisions in Article 17 permit the continued use of enzymes previously authorised under national law until the EU list is published — but this protection is temporary and will cease to apply the moment the list is formally adopted.

The problem is that the EU list has not yet been published, more than fifteen years after the Regulation entered into force. The delay results from the sheer volume of applications submitted to the European Commission and the complexity of EFSA's scientific assessments. As of mid-2026, EFSA's CEP Panel (Panel on Food Contact Materials, Enzymes and Processing Aids) continues to issue scientific opinions on individual enzymes, and the pace of this work has accelerated noticeably in recent years.

GMO strains in enzyme production: the hidden compliance risk

The majority of food enzymes used in industrial food production — including amylases, proteases, lipases and xylanases — are produced by microorganisms. In many cases, those microorganisms are genetically modified strains engineered to achieve higher enzyme yields or improved product characteristics. This is standard industrial biotechnology practice and, in itself, is not prohibited.

The compliance risk arises at the intersection of two regulatory frameworks: Regulation (EC) No 1332/2008 on food enzymes and Regulation (EC) No 1829/2003 on genetically modified food and feed. The question of which framework applies — and to what extent — has not been definitively resolved at EU level, and EFSA's evolving approach to this question is creating practical difficulties for food manufacturers.

EFSA's current position, as reflected in its scientific opinions issued under Regulation 1332/2008, is that the full characterisation of the production strain — including its GMO status, the nature of the genetic modification, and the stability of the inserted genetic elements — is a required component of the safety dossier for the enzyme itself. This requirement applies regardless of whether the final enzyme product contains any detectable DNA or protein derived from the GMO strain.

What EFSA's scientific opinions actually say

EFSA's CEP Panel has issued scientific opinions on a growing number of food enzymes in which the production strain is a GMO. These opinions follow a consistent structure: they assess the identity and purity of the enzyme, the production process, the characterisation of the production strain (including its GMO status), and the toxicological data. Where the production strain is a GMO, the Panel requires documentation equivalent to that required for a full GMO safety assessment — including molecular characterisation of the inserted DNA, expression data, and an assessment of the stability of the genetic modification over successive generations.

In a number of cases, EFSA has issued opinions concluding that the available data are insufficient to complete the safety assessment, specifically because the applicant has not provided adequate documentation of the GMO production strain. These opinions do not result in a negative conclusion on safety — rather, they place the application on hold pending supplementary data. For food manufacturers using the affected enzymes, this means that the enzyme's path to the EU authorised list is blocked until the supplier resolves the documentation gap.

Practical implications for food manufacturers

A food manufacturer using an enzyme that is subject to an incomplete or suspended EFSA assessment faces a specific set of risks. Under the transitional provisions of Article 17(3) of Regulation 1332/2008, the enzyme may currently be used lawfully — but only for as long as the EU list has not been published. Once the list is published, any enzyme not included on it will be prohibited, with no grace period for existing stocks or ongoing production runs.

The food manufacturer has no direct influence over the authorisation process — that is the supplier's responsibility. However, the food manufacturer bears full legal responsibility for ensuring that the enzymes used in their products comply with applicable law. This creates an asymmetry of risk: the manufacturer is exposed to enforcement action by the Polish Chief Sanitary Inspectorate (GIS) for using a non-authorised enzyme, even if the non-authorisation results entirely from the supplier's failure to provide adequate documentation to EFSA.

Labelling obligations: processing aids versus ingredients

A separate but related question concerns labelling obligations. Under Article 2(2)(a) of Regulation (EC) No 1169/2011 on the provision of food information to consumers, a processing aid is defined as a substance that is used in the processing of raw materials, foods or their ingredients, to fulfil a technological purpose during treatment or processing, and may result in the unintentional but technically unavoidable presence of residues of the substance or its derivatives in the final product, provided that these residues do not present any health risk and do not have any technological effect on the finished product.

Where an enzyme qualifies as a processing aid under this definition, it does not need to be declared in the list of ingredients and is not subject to the GMO labelling requirements of Regulation (EC) No 1829/2003. However, this classification is not automatic — it requires a case-by-case assessment of the enzyme's function and activity in the final product. Where an enzyme remains technologically active in the final product (for example, a protease that continues to modify protein structure after baking), it may not qualify as a processing aid and may instead need to be declared as an ingredient, with the associated GMO labelling obligations if the enzyme is produced from a GMO strain.

Supplier due diligence: what to ask and what to document

Given the risks outlined above, food manufacturers should implement a structured due diligence process for all enzymes used in their production. This process should include the following elements:

• Confirmation from the supplier of the enzyme's application status in the DG SANTE register, including the application number and the current stage of EFSA assessment.
• Disclosure of whether the production strain is a GMO, and if so, the nature of the genetic modification and the regulatory status of the strain under Regulation (EC) No 1829/2003.
• Confirmation of whether any EFSA scientific opinion has been issued in relation to the enzyme, and if so, whether the opinion identified any data gaps requiring supplementary information from the applicant.
• A contractual commitment from the supplier to notify the food manufacturer promptly of any change in the enzyme's regulatory status, including any suspension or withdrawal of the application.
• Documentation of the enzyme's function in the food manufacturer's specific production process, supporting the classification of the enzyme as a processing aid or ingredient.

This documentation should be retained as part of the food manufacturer's compliance records and made available to the Polish Chief Sanitary Inspectorate (GIS) on request.

The GIS inspection perspective

The Polish Chief Sanitary Inspectorate (GIS) has the authority to inspect food manufacturers' compliance with Regulation 1332/2008 as part of its routine official controls under Regulation (EU) 2017/625 on official controls. In practice, GIS inspectors may request documentation demonstrating that all enzymes used in production are either included on the EU authorised list or covered by the transitional provisions of Article 17(3) of Regulation 1332/2008.

Where a food manufacturer cannot demonstrate compliance — for example, because the supplier has not provided adequate information about the enzyme's application status — the inspector may treat the enzyme as unauthorised and take enforcement action accordingly. Under Article 103 of the Act of 25 August 2006 on food and nutrition safety, this may include a financial penalty of up to PLN 100,000 and an order to withdraw the affected products from the market.

It is worth noting that GIS inspectors are increasingly aware of the GMO strain issue in the context of food enzyme authorisations, following guidance issued by the Chief Sanitary Inspector and training provided by the European Commission's Better Training for Safer Food (BTSF) programme. Food manufacturers should not assume that this issue will be overlooked during inspections.

The novel food question: when does Regulation 2015/2283 apply?

A question that occasionally arises in practice is whether a food enzyme produced by a GMO strain could be subject to the novel food Regulation (EU) 2015/2283 rather than — or in addition to — Regulation 1332/2008. The answer requires careful analysis of the specific enzyme and its history of use in the EU.

As a general principle, Regulation 1332/2008 constitutes lex specialis in relation to Regulation 2015/2283 for substances that meet the definition of a food enzyme under Article 3(2)(a) of Regulation 1332/2008. However, where a substance does not meet that definition — for example, because it does not have a catalytic function in the food — or where the enzyme has no documented history of significant use in the EU before 15 May 1997, the novel food framework could apply. This scenario is most likely to arise in connection with novel enzymes derived from newly developed GMO strains, where the enzyme itself (rather than merely the production strain) is a new substance.

Conclusions and recommended actions

The wave of EFSA scientific opinions on food enzymes from GMO strains is not a temporary phenomenon — it reflects a structural feature of the EU food enzyme authorisation system that will continue to generate compliance challenges for food manufacturers until the EU authorised list is finally published. Food manufacturers should treat enzyme compliance as an active risk management issue rather than a static documentation exercise.

The recommended immediate actions are: audit all enzymes currently used in production to identify those produced by GMO strains; verify the application status of each such enzyme in the DG SANTE register; obtain written confirmation from suppliers of the current EFSA assessment status; and implement contractual mechanisms to ensure timely notification of any changes in regulatory status. Where any enzyme is found to have an incomplete or suspended EFSA assessment, the food manufacturer should assess the risk of continued use and consider identifying alternative authorised enzymes.

This is not a matter that can be safely delegated entirely to suppliers. The legal responsibility for compliance rests with the food manufacturer, and the consequences of non-compliance — financial penalties, product withdrawals, and reputational damage — are borne by the manufacturer, not the supplier.

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