A number of countries are setting legislations on mycotoxins. In order to reduce dispute between importing and exporting countries, the analytical data should be as comparable as possible, especially when levels are close to the regulatory limits. The present trend in the analysis of mycotoxins is to use immunoaffinity column (IAC) as a clean-up and enrichment technique, and Association of Official Analytical Chemists and European Union have validated methods which address a few food commodities. This study describes our experience using both conventional and IAC approaches in the analysis of three mycotoxins. Aflatoxins (AFs): Aflatoxin G1 has been detected by liquid-liquid partitioning methods with HPLC detection as false-positive in some maize. On IACs, this compound behaves as an AF, lowering the amount of the AFs trapped. The problem was solved using either TLC or HPLC with detection in the Kobra cell. Depending on the additives to food during the processing and cooking, the AFs might appear as an opened ring not recognised by the antibody. Fumonisins (FB): Compounds interfering with the FB's antibodies were also observed while analysing breakfast cereals leading to underestimation of FB. Ochratoxin A (OTA): Depending on the food composition and extraction techniques, OTA is underestimated with IAC in some breakfast cereals and coffee. These data strengthen the necessity to validate methods using IAC for each complex matrix.