Allergen Testing in the Food Industry: ELISA vs PCR and Other Methods

Food allergen management is one of the most critical aspects of food safety in the food industry. Undeclared allergens are a leading cause of product recalls worldwide. A single mistake can put consumers at risk and damage a company’s reputation.

While proper labeling and allergen segregation are important, the foundation of allergen control lies in allergen testing methods. Choosing the right method can be confusing — should you use ELISA, PCR, or a quick strip test for allergen testing in food industry?

This blog breaks down the three main allergen detection methods — Lateral Flow Devices (LFDs), ELISA, and PCR — and explains where each one is most effective.

Lateral Flow Devices (LFDs / Strip Tests) for Allergen Testing

Principle: LFDs are immunochromatographic tests where allergen proteins bind to antibodies on a strip, producing a visible line.

Application: Best for on-site, rapid checks of raw materials, processing surfaces, or finished products.

Strengths:

• Deliver results in minutes

• Easy to use, no lab equipment required

• Useful for quick in-process decision making

Limitations:

• Lower sensitivity compared to lab-based methods

• Usually qualitative (yes/no result only)

• Limited ability to test for multiple allergens

ELISA (Enzyme-Linked Immunosorbent Assay) for Allergen Detection

Principle: ELISA detects allergen proteins using antibody binding, with an enzyme-driven color change as the signal.

Application: Used widely for raw materials, finished products, and cleaning validation, especially when proteins remain intact.

Strengths:

• High specificity and reliability

• Quantitative (provides exact allergen concentration)

• Globally validated for many allergen types

Limitations:

• Heat processing or hydrolysis can degrade proteins, leading to false negatives

• Requires laboratory setup and trained technicians

PCR (Polymerase Chain Reaction) for Allergen Detection

Principle: PCR detects allergen DNA by amplifying target genetic sequences.

Application: Suitable for highly processed or complex foods where allergenic proteins may be degraded but DNA fragments remain detectable.

Strengths:

• Extremely sensitive, capable of detecting trace amounts

• Works in foods where ELISA may not detect proteins

• Useful for verifying compliance in complex supply chains

Limitations:

• Presence of DNA does not always confirm presence of allergenic proteins

• Requires specialized equipment and expertise

LFD vs ELISA vs PCR: Which Method Should You Choose for Allergen Testing in Food Industry?

• Use LFDs for rapid, on-site allergen checks.

• Use ELISA when protein-level confirmation is required, such as for finished product testing or cleaning validation.

• Use PCR for processed foods where proteins may no longer be intact but DNA fragments survive.

At a glance: LFD vs ELISA vs PCR allergen detection methods for food industry applications.

In many cases, ELISA and PCR complement each other, providing a more complete allergen management strategy.