Conventionally, epoxidation of unsaturated fatty acids has been studied either with titrimetric methods or in a lengthy procedure involving derivatization followed by gas chromatography (GC). We have developed a more rapid and descriptive analysis procedure for the substances using high performance liquid chromatography (HPLC) with evaporative light scattering detection (ELSD). Chemo-enzymatic epoxidation of unsaturated fatty acids (oleic, linoleic and linolenic acid, respectively) has been performed using hydrogen peroxide and immobilized lipase from Candida antarctica (Novozym 435). The fatty acids and their epoxidation products were separated by HPLC on a C-18 reversed-phase column using methanol-water containing 0.05% acetic acid as mobile phase. The method facilitated the simultaneous determination of fatty acids and epoxides differing from each other in the number of epoxide rings, the degree of unsaturation and the position of the epoxide rings and double bonds. An important aspect of the method development was the use of electrospray ionization and tandem mass spectrometry to confirm the structure of the epoxide products. It is suggested that the HPLC method, providing more information about the kind and concentration of fatty acids and their epoxides, represents a powerful complement to the existing methods for monitoring epoxidation processes on fatty acids.