Vaccenic acid (trans-11-C(18:1)) chemically resembles elaidic acid (trans-9-C(18:1)) which is assumed to increase the risk of cardiovascular diseases, and thus could exert similar effects. Possible different oxidation rates of vaccenic versus elaidic acid were checked in muscles and liver, and through related gene expression in normal rat liver cells. In hepatic mitochondria, carnitine palmitoyltransferase (CPT) I exhibited comparable activity rates with both trans-isomers. CPT II activity was 30% greater (P < 0.05) with vaccenic than with elaidic acid as nonesterified fatty acids (NEFAs) or acyl-CoAs. Activity of the first beta-oxidation step was similar between the isomers in all the tissue slices and liver extracts assayed. Respiration rates were comparable with both trans-isomers as NEFAs in various liver extracts, but were 30% greater (P < 0.05) with vaccenoyl-CoA than with elaidoyl-CoA in liver mitochondria. Vaccenic acid was oxidised 25% more (P < 0.05) by liver peroxisomes than elaidic acid. In hepatocytes cultured with trans- and corresponding cis-C(18:1) isomers, gene expression of CPT I, hydroxyacyl-CoA dehydrogenase and hydroxymethylglutaryl-CoA synthase was at least 100% increased (P < 0.05), but was unchanged with vaccenic acid, relative to controls. In conclusion, the position and geometry of the double bonds in acyl chains are suggested to confer on vaccenic and elaidic acid specific biochemical properties that might differently affect their fates in tissues.