Mycotoxins are toxic metabolites produced by some fungi developing on several agricultural commodities. In sub-Saharan Africa, the recent changes in feeding practices increase the risk of contamination for dairy cattle and subsequently the passage of mycotoxins in the food chain. Aflatoxins are the major mycotoxins known to enter into milk and many milk-based foods. The naturally occurring aflatoxin B is (bio-) transformed by mammals into various metabolites including the aflatoxin M excreted in milk. Food processing aiming at long term food storage (sterilization, pasteurisation, freeze-drying.) do not alter, or only slightly, the toxicity of aflatoxins. The best option to reduce milk contamination is to prevent the introduction of contaminated feed in the dairy cattle diet. Very little information is available on the flux and modifications of mycotoxins (synthesis, alteration, dilution or concentration) during the processing of milk and milk-based products. Therefore this field of research is given a high priority by the scientific community.