Reversed-phase high-performance liquid chromatography (RP-HPLC) and silver-ion high-performance liquid chromatography (Ag-HPLC) were successively combined for the separation of the longer-chain metabolites of conjugated linoleic acids (CLAs). Commercial silver nitrate-impregnated columns were used with an eluting solvent composed of a mixture of hexane-acetonitrile. Fatty acid methyl esters (FAMEs) from liver lipids of rats fed CLA were analysed. This method allowed separation both of the non-conjugated FAME, as C16:1, C18:2, C18:3, C20:4 and C22:5, but also the conjugated fatty acids like CLA, 8,12,14-20:3, 5,8,12,14-20:4 and 5,8,11,13-20:4. The presence of 8,11,13-20:3 is reported for the first time. This method is of interest for the isolation and identification of the C20 conjugated metabolites that cannot be resolved by gas chromatography. Furthermore, it allows the isolation of FAME for further characterisation by GC-mass spectrometry (MS).