An overview is given of current techniques for the analysis of organic micropollutants that accumulate in the fatty fraction of foodstuffs, such as pesticides, polychlorinated biphenyls, polycyclic aromatic hydrocarbons, polychlorinated dibenzodioxins and polychlorinated dibenzofurans. Isolation and clean-up are considered to be of great importance in the field of residue analysis. In general, problems are related to the low levels of the individual compounds at which they usually occur and the complexity of extraction and clean-up procedures for isolating and separating analytes from matrix components and other contaminants. Therefore, special attention is focused on sample pretreatment and on coupled chromatographic techniques, showing developments towards multi-residue methods, miniaturization and automation of analytical procedures. Coupling of chromatographic techniques with spectroscopic techniques is also considered as an important tool for identification and confirmation purposes.