Effects of the conjugated linoleic acid (CLA) isomers cis-9, trans-11 (c9, t11 CLA) and trans-10, cis-12 (t10, c12 CLA) on lipid metabolism and markers of peroxisome proliferation were investigated in hamsters fed on purified diets containing 30 % energy as fat and 0·1 g cholesterol/kg for 8 weeks. Four groups (n 32 each) received diets without CLA (control), with a mixture of equal amounts of c9, t11 and t10, c12 CLA (CLA mix), with c9, t11 CLA, and with t10, c12 CLA. The total amount of CLA isomers was 1·5 % energy or 6·6 g/kg diet. CLA was incorporated into glycerides and exchanged for linoleic acid in the diet. Compared with the control, the CLA mix and t10, c12 CLA decreased fasting values of LDL- (21 and 18 % respectively) and HDL-cholesterol (8 and 11 %), increased VLDL-triacylglycerol (80 and 61 %), and decreased epididymal fat pad weights (9 and 16 %), whereas c9, t11 CLA had no significant effects. All CLA preparations increased liver weight, but not liver lipids. However, the increase in liver weight was much less in the c9, t11 CLA group (8 %) than in the other two groups (25 %) and might have been caused by the small amount of t10, c12 CLA present in the c9, t11 CLA preparation. Liver histology revealed that increased weight was due to hypertrophy. Markers of peroxisome proliferation, such as cyanide-insensitive palmitoyl CoA oxidase (EC 184.108.40.206) and carnitine acetyl transferase (EC 220.127.116.11) activities, were not increased by CLA. Both c9, t11 CLA and t10, c12 CLA were incorporated into phospholipids and triacylglycerols, but t10, c12 CLA only about half as much as c9, t11 CLA. In addition, linoleic acid and linolenic acid concentrations were lower in lipids of the t10, c12 CLA group compared with the c9, t11 CLA group. These data suggest that t10, c12 CLA stimulated the oxidation of all C18 polyunsaturated fatty acids. The results indicate that the t10, c12 CLA isomer, and not the so-called natural CLA isomer (c9, t11), is the active isomer affecting lipid levels in hamsters.