Mycotoxins are of toxicological relevance and consequently important contaminants in food and feed. The most common mycotoxins with the highest toxicity are the aflatoxins (AFs), which cause liver cirrhosis or primary liver carcinomas and have been shown to be the immunosuppressive. The European Union has set the maximum levels as low as reasonably achievable to protect consumers. To perform appropriate risk assessment for AFs robust analytical methods are required to provide reliable results. Different steps in the analysis of AFs in food and feed are necessary such as sampling, extraction, sample purification and detection. Throughout the analysis chain, methods have to be precise and reproducible. The sensitivity of an analysis, especially if the detection is not selective enough depends strongly on the sample clean up. However, techniques in sample preparation and analytical methods are improving continuously. This manuscript gives an overview on different analytical methods with emphasize on sample preparation strategies used in the analysis of AFs in food and feed.