Conjugated linoleic acids (CLA) are reported to have anticarcinogenic and antiatherogenic properties. Different gas chromatographic conditions enabling extensive separation of the numerous CLA isomers were checked by using a high polar 100 m-capillary column (Sil 88). Errors in CLA quantitation, particularly caused by overlaps with cis-C20:1 isomers or C21, were discussed. Under optimal conditions, it has already been possible to separate the closely eluting isomers cis Delta 9,trans Delta 11 (c9t11) and trans Delta 9,cis Delta 11 (t9c11) in bovine and human milk fat by using a shorter medium-polar 25 m-capillary column (Wax 58) in routine analyses. Additionally, it could be demonstrated in several feeding trials with cows that an increase in the content of CLA c9t11 in milk fat is usually associated with an increase of the possibly atherogenic fatty acids trans-C18:1 and trans-C18:2. Simultaneously, a strong decrease of the medium-chain fatty acids, e.g. lauric, myristic and palmitic acid, causing an increase of the cholesterol level, was observed.