Mycotoxins in Food: Types, Regulatory Limits, Health Risks & Testing

Introduction

Mycotoxins are naturally occurring toxic compounds produced by certain species of moulds (fungi). They can contaminate agricultural commodities before harvest or during drying, storage and processing.

Mycotoxin contamination is an important food-safety concern because some mycotoxins can cause acute toxicity, while prolonged exposure to certain mycotoxins has been associated with serious health effects, including cancer, immune effects and organ toxicity.

The World Health Organization (WHO) identifies aflatoxins, ochratoxin A (OTA), fumonisins, zearalenone, patulin and deoxynivalenol (DON) among the major mycotoxins of concern in food.

Mycotoxin control therefore requires more than visual inspection for mould. Because many mycotoxins can remain present even when visible mould is no longer apparent, risk-based laboratory testing is an important part of food quality and safety programmes.

What Are Mycotoxins?

Mycotoxins are secondary metabolites produced by certain fungi that can grow on crops and food products.

Mould growth and mycotoxin formation can occur:

Before harvest
During harvesting
During drying
During transportation
During storage
During processing

Warm, humid conditions can favour fungal growth and mycotoxin formation. WHO notes that many mycotoxins are chemically stable and may survive food processing.

This means that preventing contamination at the agricultural and storage stages is generally preferable to relying only on finished-product testing.

Major Mycotoxins Found in Food

Different fungal species and environmental conditions are associated with different mycotoxins.

The occurrence of a particular mycotoxin depends on the crop, fungal species, climate, agricultural conditions and storage environment.

Aflatoxins: One of the Most Important Mycotoxin Groups

Aflatoxins are produced mainly by certain Aspergillus species. The principal aflatoxins include:

Aflatoxin B1
Aflatoxin B2
Aflatoxin G1
Aflatoxin G2

Aflatoxin B1 is particularly important from a food-safety perspective.

Aflatoxins can occur in:

Peanuts
Tree nuts
Maize
Cereals
Oilseeds
Spices
Dried foods

WHO identifies aflatoxins among the most toxic mycotoxins and notes evidence linking aflatoxin exposure with liver cancer.

Aflatoxin M1 in Milk

Aflatoxin M1 (AFM1) is different from the major aflatoxins found directly in crops.

It can occur in milk when dairy animals consume feed contaminated with aflatoxin B1. Consequently, monitoring may be relevant for:

Raw milk
Processed milk
Dairy products
Milk powder

FSSAI’s Contaminants, Toxins and Residues framework includes a specific requirement for aflatoxin M1 in milk.

Ochratoxin A (OTA)

Ochratoxin A is produced by certain species of Aspergillus and Penicillium. It may occur in:

Cereals
Cereal products
Coffee
Dried fruits
Spices
Grape products
Other stored commodities

Kidney toxicity is an important toxicological concern associated with OTA. WHO identifies kidney damage as its most notable effect in animal studies.

Deoxynivalenol (DON)

Deoxynivalenol (DON), sometimes referred to as vomitoxin, is primarily associated with cereal crops. Potential sources include:

Wheat
Maize
Barley
Other cereals

DON is particularly associated with Fusarium infection of crops.

Monitoring can be important for cereal-based ingredients and finished products, particularly where raw materials are sourced from regions or seasons with elevated fungal risk.

Fumonisins

Fumonisins, particularly fumonisin B1 and B2, are commonly associated with maize and maize-based products.

Their occurrence is influenced by fungal infection and environmental conditions during crop production and storage.

Fumonisins are among the major mycotoxins monitored internationally and are included in food-safety risk assessments and regulatory frameworks.

Zearalenone

Zearalenone (ZEN) is another mycotoxin associated primarily with Fusarium species and cereal crops.

It is known for its estrogenic activity, meaning it can interact with estrogen receptors. Testing may be relevant for:

Wheat
Maize
Barley
Cereal products
Cereal-based ingredients

Patulin

Patulin is primarily associated with mould-damaged fruits, particularly apples. It is therefore relevant to:

Apples
Apple juice
Apple puree
Fruit preparations
Other fruit products

WHO identifies patulin as one of the important food-related mycotoxins, while regulatory frameworks establish maximum levels for specific fruit products.

Health Risks Associated with Mycotoxins

The health effects of mycotoxins depend on:

Type of mycotoxin
Concentration
Duration of exposure
Frequency of consumption
Individual susceptibility
Age
Nutritional status

Potential effects can range from acute poisoning to chronic health effects.

WHO reports that mycotoxin exposure can result in effects including acute illness, immune effects and cancer, depending on the specific toxin and exposure.

Examples

Aflatoxins: Liver toxicity and carcinogenicity
Ochratoxin A: Kidney toxicity and possible developmental/immune effects
DON: Gastrointestinal and other toxic effects
Fumonisins: Toxicological effects affecting multiple biological systems
Zearalenone: Estrogenic effects
Patulin: Toxicological effects associated particularly with contaminated fruit products

EU Regulatory Requirements for Perchlorate

Mycotoxin contamination can develop at multiple stages.

Before Harvest

Weather conditions, crop stress, insect damage and fungal infection can increase contamination risk.

During Harvest

Damaged or improperly harvested crops may become more susceptible to fungal growth.

During Drying

Insufficient drying can leave moisture levels favourable for mould growth.

During Storage

High humidity, temperature fluctuations, insects and poor storage conditions can promote fungal development.

During Transportation

Improper environmental conditions during transport can contribute to moisture accumulation and fungal growth.

Can Mycotoxins Be Removed by Processing?

Not always.

One of the important challenges with mycotoxins is their chemical stability. WHO notes that many mycotoxins can survive food processing. Therefore, food businesses should not assume that:

Processing automatically eliminates mycotoxin contamination.

The most effective strategy is generally to prevent or minimize contamination at the agricultural, drying and storage stages and then verify compliance through appropriate testing.

Regulatory Limits for Mycotoxins

Mycotoxin limits are not universal.

The applicable maximum level depends on:

Mycotoxin
Food commodity
Product category
Intended use
Destination market
Applicable legislation

Therefore, exporters should always verify the current commodity-specific requirement before assessing compliance.

In India, mycotoxins are addressed primarily under the Food Safety and Standards (Contaminants, Toxins and Residues) Regulations, 2011, as amended.

FSSAI’s regulatory framework includes limits for contaminants and naturally occurring toxic substances, including aflatoxins, aflatoxin M1, patulin and other relevant substances.

FSSAI’s official amendment history also shows continued updates to the Contaminants, Toxins and Residues framework, including an amendment published in May 2026 relating to metal contaminants, naturally occurring toxic substances and antibiotic residues.

Important Compliance Point Food manufacturers should use the latest applicable FSSAI regulation/compendium when determining the legal limit for a specific product rather than relying on an old laboratory specification or historical article.

The European Union regulates maximum levels for several mycotoxins through Commission Regulation (EU) 2023/915 on maximum levels for certain contaminants in food.

The regulation establishes commodity-specific maximum levels for relevant contaminants, including several mycotoxins.

Depending on the commodity, EU controls can cover substances such as:

Aflatoxins
Ochratoxin A
Deoxynivalenol
Zearalenone
Fumonisins
T-2 and HT-2 toxins
Patulin

The applicable level must be checked against the specific product category and current version of the regulation.

For exporters, this is particularly important because the same mycotoxin may have different limits depending on the food category.

The Codex Alimentarius Commission, supported by scientific risk assessments from the Joint FAO/WHO Expert Committee on Food Additives (JECFA), develops international standards and guidance for controlling mycotoxin exposure.

WHO notes that Codex maximum levels for mycotoxins are based on JECFA risk assessments and are used internationally as reference points for food safety and trade.

However, national and regional regulations may establish different requirements.

Therefore:

Codex ≠ automatically applicable legal limit in every country.

Exporters should always check the legislation of the destination market.

How Are Mycotoxins Tested?

Laboratory analysis is essential because visual inspection alone cannot reliably determine the concentration of mycotoxins. Common analytical approaches include:

HPLC

High-Performance Liquid Chromatography can be used for quantitative determination of several mycotoxins, depending on the analytical method and detector configuration.

LC-MS/MS

Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) provides highly selective and sensitive determination of multiple mycotoxins.

It can be particularly useful for multi-mycotoxin screening, where several compounds need to be analysed simultaneously.

Immunoassay-Based Screening

Techniques such as ELISA may be used for screening applications.

Where regulatory or confirmatory analysis is required, an appropriate validated instrumental method may be necessary.

Multi-Mycotoxin Testing

A major advantage of modern LC-MS/MS approaches is the ability to analyse multiple mycotoxins within a single analytical programme.

A multi-mycotoxin panel may include combinations of:

Aflatoxin B1
Aflatoxin B2
Aflatoxin G1
Aflatoxin G2
Aflatoxin M1
Ochratoxin A
DON
Zearalenone
Fumonisins
T-2 toxin
HT-2 toxin
Patulin

The exact panel should be selected according to the commodity, geographical risk, regulatory requirement and customer specification.

Why Sampling Is Critical in Mycotoxin Testing

Mycotoxin contamination can be heterogeneous.

This means that contamination may not be evenly distributed throughout a batch. As a result, the reliability of the final laboratory result depends not only on the analytical method but also on:

Sampling → Sample Preparation → Homogenisation → Extraction → Analysis

An excellent analytical instrument cannot compensate for a poorly representative sample.

For this reason, appropriate sampling and homogenisation procedures are critical components of a mycotoxin testing programme.

Important Analytical Parameters

A laboratory method should be appropriate for the intended food matrix and regulatory requirement.

Important analytical performance characteristics include:

Specificity
Accuracy
Precision
Recovery
Linearity
Limit of Detection (LOD)
Limit of Quantification (LOQ)
Matrix effects
Measurement uncertainty
Quality-control performance

For regulatory compliance, the method should provide an LOQ appropriate to the applicable maximum level.

When Should Food Businesses Test for Mycotoxins?

Testing can be incorporated throughout the supply chain.

Reduce crop stress, insect damage and fungal infection where possible.

Dry susceptible commodities rapidly and adequately after harvest.

Maintain appropriate temperature and humidity conditions.

Control insects and pests that can damage crops and facilitate fungal invasion.

Assess suppliers based on agricultural practices, storage conditions and historical analytical performance.

Maintain traceability from raw material through finished product.

Increase testing for commodities, suppliers or regions associated with higher mycotoxin risk.

How Eureka Supports Mycotoxin Testing

Eureka supports food manufacturers, ingredient suppliers, exporters and other food businesses with analytical testing for mycotoxins and related food contaminants.

Mycotoxin Testing Support

Depending on the product and requirement, testing can include:

Aflatoxins
Aflatoxin M1
Ochratoxin A
Deoxynivalenol (DON)
Fumonisins
Zearalenone
T-2 and HT-2 toxins
Patulin
Other relevant mycotoxins

Relevant Food Matrices

Testing programmes can be designed for relevant products such as:

Cereals
Pulses
Spices
Nuts
Oilseeds
Dried fruits
Coffee
Fruit products
Milk and dairy products
Processed foods
Food ingredients
Nutraceutical and botanical ingredients

Compliance Applications

Eureka can support:

Raw-material qualification
Supplier verification
Batch-release testing
Regulatory compliance
Pre-export testing
Customer specification testing
Contamination investigation
Risk-based monitoring programmes

The appropriate analytical panel and acceptance criteria should be determined according to the commodity, applicable regulation, destination market and customer requirement.

Building a Risk-Based Mycotoxin Control Programme

A practical approach can follow:

Identify Risk → Qualify Supplier → Control Storage → Select Appropriate Panel → Sample Correctly → Analyse → Compare Against Applicable Limit → Investigate Deviations → Maintain Traceability

This approach helps businesses move from reactive testing to preventive food safety management.

Key Takeaways

Mycotoxins are naturally occurring toxins produced by certain moulds.
Major food-related mycotoxins include aflatoxins, OTA, DON, fumonisins, zearalenone and patulin.
Mycotoxin contamination can occur before harvest and during drying, storage and transportation.
Many mycotoxins can remain stable during food processing.
Aflatoxin B1 is a major food-safety concern because of its liver toxicity and carcinogenicity.
Regulatory limits vary according to the mycotoxin, commodity and destination market.
India regulates relevant mycotoxins under the FSSAI Contaminants, Toxins and Residues framework.
The EU establishes commodity-specific maximum levels under Regulation (EU) 2023/915.
LC-MS/MS can support sensitive multi-mycotoxin analysis.
Sampling and homogenisation are critical because mycotoxin contamination can be unevenly distributed.
Effective mycotoxin control combines supplier management, agricultural controls, proper drying and storage, representative sampling and laboratory testing.

Frequently Asked Questions (FAQ)

1. What are mycotoxins?

Mycotoxins are toxic compounds naturally produced by certain moulds that can contaminate crops and food products.

2. Which foods are commonly affected by mycotoxins?

Cereals, nuts, spices, oilseeds, dried fruits, coffee, milk and other agricultural commodities can be affected, depending on the specific mycotoxin and environmental conditions.

3. What are the most important mycotoxins in food?

Commonly monitored mycotoxins include aflatoxins, aflatoxin M1, ochratoxin A, deoxynivalenol, fumonisins, zearalenone, T-2/HT-2 toxins and patulin.

4. Are mycotoxins destroyed during food processing?

Not necessarily. Many mycotoxins are relatively stable and may survive certain processing conditions.

5. What is the regulatory limit for mycotoxins?

There is no single universal limit. The applicable limit depends on the specific mycotoxin, food commodity and regulatory jurisdiction.

6. How are mycotoxins detected?

Depending on the target toxin and matrix, laboratories may use techniques such as LC-MS/MS, HPLC or immunoassay-based screening methods.

7. Why is sampling important for mycotoxin testing?

Mycotoxin contamination can be unevenly distributed within a batch. Representative sampling and proper homogenisation are therefore essential for obtaining a meaningful laboratory result.

8. Should exporters test mycotoxins before shipment?

For high-risk commodities and destinations with stringent requirements, pre-export testing can help verify compliance before shipment.

9. Can multiple mycotoxins be tested together?

Yes. Multi-mycotoxin LC-MS/MS methods can allow several mycotoxins to be assessed within a single analytical programme, subject to the laboratory’s validated scope.

10. How can Eureka support mycotoxin testing?

Eureka can support food manufacturers, ingredient suppliers and exporters with targeted and multi-mycotoxin testing for relevant food matrices, helping with raw-material qualification, quality control, regulatory assessment and export compliance.

Official References

Food Safety and Standards Act, 2006
Food Safety and Standards (Contaminants, Toxins and Residues) Regulations, 2011, as amended
FSSAI – Compendium of Food Safety and Standards (Contaminants, Toxins and Residues) Regulations
Commission Regulation (EU) 2023/915 on maximum levels for certain contaminants in food
Regulation (EC) No 1881/2006 – Maximum levels for certain contaminants in foodstuffs (historical framework; replaced by Regulation (EU) 2023/915)
Codex Alimentarius Commission – General Standard for Contaminants and Toxins in Food and Feed (CXS 193-1995)
FAO/WHO Joint Expert Committee on Food Additives (JECFA) – Mycotoxin Risk Assessments
World Health Organization (WHO) – Mycotoxins
International Agency for Research on Cancer (IARC) – IARC Monographs on the Evaluation of Carcinogenic Risks to Humans

Conclusion

Mycotoxin contamination remains a significant food-safety and trade-compliance challenge because contamination can occur at multiple points from crop production through storage and processing.

A robust control strategy should therefore combine preventive measures with appropriate analytical verification.

For manufacturers and exporters, the key is not simply to ask “Is my product tested for mycotoxins?” but rather:

Which mycotoxins are relevant to my commodity? What regulatory limit applies to my destination market? Is my sampling representative? And does my analytical method provide sufficient sensitivity to demonstrate compliance?

By combining supplier controls, proper storage, representative sampling and validated laboratory analysis, food businesses can strengthen mycotoxin risk management and support safer, more compliant products.

Eureka Analytical Services can support this process through risk-based mycotoxin testing, multi-mycotoxin analysis and food contaminant testing tailored to the product and intended market.