Mycotoxins are natural substances produced as secondary metabolites by a wide variety of different species of filamentous fungi. One of the most important groups in terms of occurrence and toxicity, is the group of aflatoxins (AFs). The major members of this group are aflatoxin B1, B2, G1, G2, M1 and M2. Exposure to AFs can cause chronic and acute toxic effects or death, as they can be carcinogenic, mutagenic, teratogenic and immunosuppressive. AFB1 is considered as the strongest carcinogen of natural origin and it is normally predominant in crops as well as in food products. Aflatoxin M1 is a major metabolite of aflatoxin B1 in humans and animals and it may be present in milk from animals fed with contaminated feed. Although the toxicity of M1 is about ten times lower than B1, it is known for its hepatotoxic and carcinogenic effects. Solid phase extraction (SPE) or the clean-up with organic solvents or immunoaffinity columns (IAC) have been frequently applied in the analysis of mycotoxins from cereals and/or milk. IAC in combination with HPLC are increasingly used as reference method due to their high selectivity and good elimination of matrix interferences. However, the cost of analysis is usually high. In recent years, molecularly imprinted polymers (MIP) have been become very popular and promising materials for extracting different analytes. AFs are too toxic to be used in MIP preparation and template bleeding may be an additional problem, especially when dealing with very low levels. For this reason, a dummy template was preferred for MIP synthesis. A rapid and selective extraction method based on magnetic MIP (MMIP) has been developed for the isolation of aflatoxins (B1, B2, G1, G2, M1) using a combination of imprinted polymer and magnetite. The successful MMIP stirring “cake” (used as a stir-bar) has been combined with HPLC-MS/MS for the determination of AFM1 in milk powder (infant formulas) to demonstrate its applicability to real samples.