A novel procedure is described for the derivatization of fatty acid epoxides in the presence of their corresponding diols. The acidic character of 2,3,5,6-tetrafluorobenzenethiol promotes favorable mass fragmentation of linoleate and arachidonate derived epoxide derivatives and reduces alkene isomerization to a manageable side reaction, eliminated through the addition of a thiol scavenger. After silylation, regioisomeric mixtures of epoxy- and dihydroxylipids are simultaneously detected and discriminated using gas chromatography with electron impact mass spectral detection. Silylated hydroxysulfanyloctadecanoids yielded instrumental detection limits of 5 pg/microl, sufficient sensitivity for the quantification of endogenous epoxylipids.