A high-performance liquid chromatographic (HPLC) method is described for the determination of conjugated linoleic acids (CLA) and conjugated linolenic acids (CLN). Methyl esters prepared from purified lipid fractions of soybean oil were analyzed using an HPLC system equipped with photodiode-array detector to detect peaks having maximum absorption around 233 and 275 nm. These peaks were concentrated by AgNO3-silicic acid column chromatography and reversed-phase HPLC. The structural analysis, of dimethyloxazoline (DMOX) derivatized methyl esters, using gas chromatography–mass spectrometry (GC–MS) showed the occurrence of 9,11- and 10,12-CLA and 8,10,13-, 8,10,12-, and 9,11,13-CLN. The comparison of these conjugated fatty acids with authentic isomers by HPLC revealed the presence of isomeric mixtures of CLA [cis (c),trans(t) or t,c and t,t] and CLN (c,t,t or t,t,c and t,t,t). Traces of 9,11- and 10,12-CLA (c,t or t,c) were found in crude oil. CLN isomers (8,10,12-18:3 and 9,11,13-18:3) were found to be forming during the bleaching phase of soybean oil processing. 8,10,13-CLN and 9,11- and 10,12-CLA (t,t) were only found in soybean oil after the deodorization step. CLN contents in commercial soybean oil varied from 387 to 1,316 mg/kg oil. A decreased level of bleaching earth and temperature resulted in a reduced CLN content. It is possible that CLN would be derived from the linoleate hydroperoxides formed during the processing and storage of soybean oil.