FDA releases draft guidance on food allergen programs under the Preventive Controls rule

The U.S. Food and Drug Administration (FDA) recently issued a new food allergen-focused chapter of its Hazard Analysis and Risk-Based Preventive Controls for Human Food draft guidance.1The new chapter addresses allergen cross-contact controls, label controls, allergens controlled under a supply-chain program, and allergen advisory statements.  Although the draft guidance provides detailed recommendations with many examples, it is not intended to be a prescriptive listing of required programs.  Instead, it is written with the goal of assisting companies to develop food allergen programs that are appropriate to their operations.  FDA notes the recommendations also may be useful when developing programs that address substances that are associated with food sensitivities (e.g., yellow 5, sulfites).  Comments on the draft guidance are requested by March 26, 2024.

This update provides an overview of the major sections of the 108-page long draft guidance.  Although not summarized herein, note that FDA also provides in the draft guidance two detailed case studies of food allergen programs (for a commercial dessert manufacturer and commercial bakery) that provide further insights into the how the content of the draft guidance could be applied in practice.  In many instances the draft guidance identifies FDA expectations for allergen controls that may go beyond what many companies are doing today under their food safety plans.  In this summary we try to highlight many of these statements.  Careful review of the draft guidance, however, is recommended as it sets forth FDA’s expectations regarding allergen programs. 

General Considerations for Allergen Programs

The control of major food allergens is one of the foundational programs in the requirements established by 21 CFR Part 117.  When FDA updated the general current Good Manufacturing Practices (GMPs) in Subpart B (i.e., 21 CFR 117.10-117.110) the agency added numerous provisions that address the handling and control of major food allergens.  The preventive controls requirements of 21 CFR Part 117 (i.e., 21 CFR 117.1126-117.190) are similarly focused on controlling major food allergens under a food safety plan.  In the draft guidance FDA explains major food allergens are treated as a chemical hazard under a hazard analysis when they are present inadvertently or when the label does not declare every major food allergen in the product.  The draft guidance focuses on the unintended allergen presence that can occur through failure to prevent allergen cross-contact between foods that contain different major food allergen profiles.  In one of the examples of inadvertent cross-contact, FDA advises the food allergen program should be designed to reduce the potential for dust from powder milk ingredients when the dust has the potential to spread to foods that do not contain milk.  While FDA does not assert the food safety plan must have a preventive control to address dust, the statement would support an FDA expectation that the hazard analysis should consider dust contamination when handling powder ingredients derived from major food allergens.

The draft guidance also sets the agency expectations for advisory labeling such as “may contain” statements.  FDA reiterates such statements cannot be used in lieu of GMPs and they must be truthful and not misleading.  In instances when a company uses an advisory statement, FDA states “your preventive controls qualified individual (PCQI) should provide a written justification, in your food safety plan, for why allergen cross-contact controls cannot ensure protection of food from allergen cross-contact.”  FDA similarly addresses advisory labeling from suppliers and states you should not approve such suppliers unless you determine they cannot control inadvertent cross-contact through GMPs.  The agency statement reinforces the agency position that when advisory labeling is used, the agency will expect the company to have data documenting the inability to prevent cross-contact through GMPs.

FDA recognizes it has not established thresholds  for major food allergens that would not trigger an allergen declaration.  FDA does recognize published data on population threshold dose responses to various food allergens “are becoming increasingly available” and they “may raise the possibility that some low-level exposures to food allergens, and the presence of certain allergen-derived ingredients, may not cause allergic reactions in most consumers who have the food allergen.”  FDA recognizes food manufacturers could evaluate such data in light of their specific products and use risk assessment or other scientifically valid assessments on appropriate food allergen controls.  While the agency has not specifically recognized allergen thresholds, the statement reinforces the agency’s willingness to consider the underlying data and recognize that very low levels of major food allergens, when unlikely to cause an allergic reaction in most consumers, would not trigger allergen controls.

The draft guidance would establish three types of preventive controls for major food allergens:  (1) allergen cross-contact controls, (2) label controls, and (3) supply chain controls when a food allergen in the ingredient or raw material is controlled prior to receipt.   Once a preventive control is established, FDA explains the importance of monitoring the preventive control with adequate frequency to provide assurance it is consistently performed.   In addition, FDA notes you must verify the preventive controls are consistently implemented and are effectively and significantly minimizing or preventing the hazard.  FDA notes Part 117 does not require the implementation of both a monitoring and verification activity for  major food allergens “when the same activity (such as visual observation) would be used as both a monitoring activity and a verification activity.”  The draft guidance also addresses the corrective actions, preventive control management components to supply chain controls, reanalysis, and records.

Allergen Cross-Contact Controls

With respect to allergen cross-contact controls, the draft guidance discusses how allergen cross-contact preventive controls are complementary to allergen cross-contact GMP programs.  A hazard analysis should consider how GMPs prevent allergen cross-contact, and preventive controls should complement and enhance those measures.  The draft guidance focuses on two key issues related to allergen cross-contact controls, each explained in more detail below: (1) allergen cleaning procedures, and (2) allergen ingredient procedures.  

Allergen Cleaning Procedures

As with all preventive controls, allergen cleaning procedures must be written and have associated management components – i.e., monitoring, verification, and corrective actions.  The draft guidance recognizes throughout that there is flexibility in how the management components are applied for all aspects of allergen preventive controls.  For example, with allergen cleaning observing that a food contact surface is visibly clean could be classified as monitoring or verification. The guidance provides several examples of activities that could be considered monitoring or verification activities for allergen cleaning procedures, including using ATP swabs, protein swabs, or allergen specific test kits to detect food residues “that remain after cleaning,” suggesting the testing should be conducted after each cleaning.  In addition, the guidance recognizes the use of “push-through” techniques and testing the “push-through” material or first product off the line. FDA also explains that forms used to document monitoring and verification activities also can function as a written procedure for those activities, and provides examples of monitoring and verification activities related to allergen cleaning.  FDA also suggests “periodically using an allergen specific test kit” after cleaning by testing swabs of food contact surfaces, final rinse water, push-through, or first product produced after push-through to demonstrate the food allergen from the previous product run has been removed. 

The agency recommends that companies develop a sanitation standard operating procedure (SSOP) that includes all procedures and forms applicable to allergen cleaning procedures that are implemented as a preventive control.  The draft guidance includes a list of potential components of the SSOP, including cleaning frequency, personnel responsible, cleaning instructions, monitoring and verification activities, corrections or corrective actions, and applicable forms.

The draft guidance discusses the role of corrections and corrective actions related to allergen cleaning.  FDA recommends that corrective action procedures distinguish between those corrective actions you would take if you determine that the problem was due to improper implementation of the allergen cleaning procedure (e.g., occasional findings of product residue on a cleaned food contact surface) and those corrective actions you would take if you determine that the allergen cleaning procedure is not effective (e.g., repeated findings of product residue on a cleaned food contact surface).  Reanalysis of the allergen cleaning procedures also could be triggered if, “for example, repeated findings of product residue on a cleaned [food contact surfaces] lead you to determine that the cleaning procedure is not effective.”

Allergen Ingredient Procedures

Allergen ingredient procedures can be used to complement the GMP requirement that raw materials and other ingredients that are food allergens, and rework that contains food allergens, be identified an held in a manner that prevents allergen cross-contact.  FDA explains that such procedures can be particularly useful when it is not readily apparent (either to production personnel or consumers) that an ingredient is or contains a food allergen.  For example, such procedures may apply if ingredients are transferred from their original packaging to containers used in production.  FDA advises reanalysis of the ingredient procedures would be appropriate for example, with “repeated findings that an allergenic ingredient was unintentionally added to your food product.” 

Label Controls

For label controls, FDA recommends a focusing on both (1) the product label itself, so that it correctly names the food source of all ingredients that are, or contain, a major food allergen, and (2) applying the correct label to the correct product.  The draft guidance identifies detailed examples of procedures that could be implemented for every stage of the labeling process.

  • Label development (e.g., identifying any allergenic ingredients in the formulation, identifying raw materials or other ingredients from suppliers with allergenic components).  In instances when a label bears an advisory statement, FDA recommends the PCQI prepare a written justification as to why the cross-contact cannot be avoided.  FDA similarly recommends the PCQI prepare a written statement regarding “your approach to allergen advisory label from a supplier.  
  • Ordering (e.g., requiring proofs; specifying procedures to reduce commingling of different product labels).  Examples of activities provided by FDA include “specifying in the written purchase document that ‘proofs’ or samples of product labels need to be  provided for your review before you authorize the initial product run of pre-printed labels” and “specifying in the written purchase document any necessary procedures to minimize the potential for commingling product labels for different products.”
  • Production (for self-generated labels) (e.g., ensuring the correct file is used for the label; limiting personnel who can edit product labels).
  • Receipt of labels is identified in a footnote as stage when it may be appropriate to conduct a monitoring or verification activity of a label control established at an earlier stage such as production rather than a separate label control.
  • Storage (e.g., preventing commingling of different product labels; labeling storage bins with a copy of the product label; promptly disposing out-of-date production labels).
  • Food production (e.g., checking a sample product label to confirm it is the correct product label; identifying labels appropriately to ensure they are used in the appropriate production line).
  • Post-production (e.g., appropriately storing unused labels after the production run is complete).

The draft guidance underscores that there is flexibility when applying preventive control management components for label controls.  Accordingly, the agency provides a combined list of examples of monitoring and verification activities without classifying the activities in either category. For example, an activity such as checking a product label received from a supplier against the food allergen label specification could generally be classified as either a monitoring activity (“monitoring” the content of the product label) or a verification activity (“verifying” the content of the product label).  However, the draft guidance also explains that some activities are more commonly considered as monitoring or verification, and are not so flexible (e.g., checking that the right label is being applied during a production run would be monitoring and reviewing those records would be verification). 

FDA offers numerous examples of monitoring and verifying label controls in the draft guidance that should be reviewed, including the statements below that provide insight into the nature of activities the agency is expecting companies to implement.   

  • “We recommend that you put a hold on product labels/packages that you receive, or the product labels that you generate yourself, until you compare them to your food allergen label specification by manually.”
  • “We recommend that you visually check that labels/packages brought to the staging area are the correct labels/packages for the product and also confirm the correct label is being applied through the use of a bar code or a manual confirmation.”
  • “We recommend that you monitor or verify the content of the product label before you use it for production by comparing the product labels/packages to your food allergen label specification at one or more of the following stages:  (1) upon receipt of the label, (2) before new batches of labels are released for use during production, or (3) immediately prior to production.”

FDA also discusses the role of corrections and corrective actions for label controls. For example, a correction may suffice if you determine that the content of a label is incorrect with respect to allergen labeling prior to use of the label, such that no food is affected. In contrast, if such a label has been used in production, a corrective action would be needed.

With respect to recordkeeping and documentation, it is notable that FDA recognizes the use of exception records as a monitoring activity, such as only keeping a record when the scanner detects the wrong label is applied to the product.

Supply-Chain Program

The draft guidance recommends that a supply-chain applied preventive control be implemented “if it is reasonably foreseeable that the food allergen profile(s) of food products produced by a potential supplier could lead to allergen cross-contact in raw materials or other ingredients that you would receive from that supplier.”  Thus, the agency expects that suppliers’ food allergen programs (including GMPs and preventive controls for allergen cross-contact) will be carefully evaluated to assess the potential for allergen cross-contact.  If a supplier provides allergen advisory statements, the receiving facility is expected to discuss the reasons for the advisory statement with the supplier before approving them and only approve them as a supplier if they determine the statements are not being used in lieu of adherence to the GMPs or allergen cross-contact control requirements.

The draft guidance provides a table with examples of supplier approval activities and ongoing supplier verification activities. FDA says that because most food allergen hazards present a risk of serious adverse health consequences or death to humans (SAHCODH), an annual audit will usually be the appropriate supplier approval and verification activity.  The draft guidance provides detailed recommendations for aspects of a supplier’s program that should be evaluated through an audit when an allergen is being controlled (e.g., ingredient storage; production scheduling; post-cleaning allergen verification). 

Notably, FDA also discusses the role of product testing as a verification activity.  For an ingredient with an allergen advisory statement, the agency encourages product testing as part of an evaluation of whether to carry forward the advisory statement.  FDA notes, “product testing for the food source that is the subject of the advisory statements can provide you with information about the frequency with which the applicable food allergen is present in the raw materials or other ingredients that you receive and,  when the food allergen is present, about the levels of the applicable food allergen.”  Multiple tests on the ingredients would be needed to collect this type of information.  The testing data could then be used by the PCQI to determine whether to carry the advisory labeling forward to your products.  In the case studies accompanying the draft guidance, FDA provides an example of a situation when a PCQI determines not to carry forward an advisory label.  FDA recommends monthly testing of the ingredient to determine whether to conduct a reanalysis of the decision not to carry forward the advisory label or to re-evaluate the supplier.  For an ingredient without such an advisory statement but for which a review of the supplier’s allergen program suggests there is a moderate or high potential for cross-contact, FDA recommends ongoing testing to verify appropriate protections are being implemented to mitigate the risk of cross-contact.  FDA notes the frequency of such testing “could vary with the potential that the ingredient would not be protected from allergen cross-contact.”

There also is a notable discussion about allergen thresholds when considering supplier controlled allergens, stating: “FDA has not established a maximum amount of food allergen that may be present in labeled food products without need for declaration. However, FDA recognizes that published data on population threshold dose responses to various food allergens are becoming increasingly available. These published data raise the possibility that some low-level exposures to certain food allergens, and the presence of certain allergen-derived ingredients, may not cause allergic reactions in most consumers who have that food allergy.”  The draft guidance goes on to explain that “food manufacturers/processors could evaluate such data in light of their specific products, such as through risk assessments or other scientifically valid scientific assessments, in making decisions on appropriate food allergen controls.”

FDA also explains that a supply-chain program for control of a food allergen hazard would not be expected if the supplier either (i) does not handle any food allergens, or (2) only manufactures/handles a single food allergen (e.g., you source almonds from a facility that only processes almonds).

FDA discusses reanalysis in the event of ongoing supplier nonconformance.  FDA considers reanalysis of the supply chain program appropriate when a supplier does not provide an advisory statement and (1) “you repeatedly detected an unintended allergen presence during routine sampling and testing of those raw material or other ingredients” or (2) you detect levels of the major food allergen during routine sampling that “are sufficiently high.”  In both of these situations, FDA identifies a discussion with the supplier about whether they have the appropriate GMP measures and allergen cross-contact controls in place.  During the reanalysis, FDA notes the PCQI should determine whether to discontinue the use of the supplier.

Allergen Advisory Statements

In 1996, FDA addressed the practice of some manufacturers to voluntarily label their products with allergen advisory statements, such as “may contain [allergen].”  In a notice to manufacturers, FDA explained that allergen advisory statements of this nature are not a substitute for, and should not be used in place of adherence to GMPs.  In addition, these statements are not a replacement for food allergen preventive controls and must be truthful and not misleading. 

In its draft guidance, FDA reiterates this policy and acknowledges that there may be some circumstances where, despite implementation of appropriate allergen GMPs and allergen cross-contact controls, a manufacturer is unable to provide assurance that the food can be protected from allergen cross-contact.  In these situations, FDA recommends providing a written justification in the food safety plan as to why allergen cross-contact controls cannot ensure food safety, and the product’s label should include information that discloses the possible unintended allergen presence in the food.  Additionally, the draft guidance addresses supplier approval when the supplier uses an allergen advisory statement, including addressing as part of the food safety plan a determination of whether the advisory statement does not impact the finished product’s allergen profile (e.g., the allergen is already an ingredient), the advisory statement will be carried forward, or the manufacturer will rely on a scientifically valid determination that the amount of the food allergen that may be present in the product is low enough so as to not cause allergic reactions in most consumers with the relevant food allergy.

Other Highlights

The draft guidance provides two examples of a food allergen program that would be implemented for a producer of ice cream and other frozen dessert products and a bakery that produces various type of cookies.  The examples should be reviewed carefully because they provide insight on the agency’s expectations of developing a model food allergen program.  The draft guidance also contains an Appendix that provides insight on the type of GMPs FDA would expect establishments to implement to prevent allergen cross-contact.  Again, the Appendix should be reviewed critically to better understand the agency’s expectations for allergen GMPs.  Below, we highlight various statements that we thought you would find of interest.

  • Assign employees to work exclusively with foods containing the same allergen profile or establish procedures for employees to change apparel when they move between areas that are processing foods with different allergen profiles.
  • Provide disposable gloves for workers who handle foods with major food allergens and advise workers to dispose of the gloves in a covered waste can after use.
  • Develop traffic patterns to restrict movement between areas that process foods with different major food allergen profiles.
  • Provide separate break areas for employees who work in processing areas handling foods with different major food allergen profiles.
  • Have physical separation for lines processing foods with different allergen profiles such as a dedicated plant, section of a plant, or processing line that is separated.
  • Use of enclosed lines or configure open production lines so they do not cross over other lines to minimize cross-contact.
  • Use of air flow controls to prevent airborne particulate matter that is, or contains, a food allergen from being brought into areas that do not use that food allergen.
  • Inspect equipment after each cleaning to determine whether it is visibly clean and periodically confirm the results of the visible inspection through periodic (e.g., quarterly) analytical tests.
  • Inspect allergen containing raw materials on receipt to ensure the containers are intact.
  • Clearly identify allergen-containing raw materials that distinguishes foods with different allergen profiles.
  • Establish and implement measures for receipt of major food allergens in containers that are not completely enclosed, such as rail cars or tankers, to ensure they are transported and transferred in a way that does not result in allergen cross-contact.
  • Segregate allergen-containing raw materials and other ingredients from raw materials that do not contain allergens. 
  • Stage allergen-containing raw materials and other ingredients in designated areas as close to the production area before opening, weighting, or transferring.
  • Place special emphasis on the control of WIP and re-work that contain food allergens.

The draft guidance provides valuable insight into the agency’s thinking with regard to the type of food allergen controls that should be implemented under the GMPs and the food safety plan.  Establishments should review the draft guidance in detail.  We also would encourage establishments to submit comments to FDA, particularly if there are agency positions or statements that could impose burdens that would be challenging to implement given the design of a manufacturing facility or other factors.

If you have any questions, please contact us.


Authored by Martin Hahn, Maile Gradison, Elizabeth Fawell, and Erin Pannek

1 FDA, Hazard Analysis and Risk-Based Preventive Controls for Human Food: Draft Guidance for Industry, Chapter 11: Food Allergen Program, FDA.gov (Sept. 26, 2023) available at https://www.fda.gov/regulatory-information/search-fda-guidance-documents/draft-guidance-industry-hazard-analysis-and-risk-based-preventive-controls-human-food.
Martin Hahn
Washington, D.C.
Maile Gradison
Washington, D.C.
Elizabeth Fawell
Washington, D.C.
Erin Pannek
Washington, D.C.
Languages English
Countries United States


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