The influence of selenium (as Na₂SeO₄) and/or conjugated linoleic acid isomers (CLA) on relative body mass gain of rats, liver weight, concentrations of CLA isomers and of other fatty acids in the rat liver were investigated. Feeding selenium (Se) and/or CLA resulted in small changes in the relative body mass and liver mass gain of rats. The administered CLA isomers significantly elevated the concentration of CLA isomers and non-CLA fatty acids containing conjugated double bonds (CFA) in the liver. Addition of Se to a diet enriched in CLA isomers generally stimulated the accumulation of CLA isomers and CFA in the liver. Our results demonstrate that the trans-trans CLA isomers are catabolized more slowly and are poor substrates for β-oxidation. The cis-trans/trans-cis CLA isomers are rapidly metabolized to form longer-chain fatty acids containing conjugated double bonds, and are partly β-oxidized. Dietary supplementation to 1% of a mixture of CLA isomers or individual CLA isomers, regardless of the presence of Se in the diets, resulted in a reduction of the sum of all assayed fatty acids, saturated fatty acids (SFA), PUFA and MUFA. Our study demonstrated that dietary CLA isomers, regardless of the presence Se in the diet, caused a reduction in Δ9-desaturase capacity, inhibited steaoryl-CoA desaturase mRNA expression, and fatty acid synthesis. As a result, the value of the concentration ratio of oleic acid to C18:0 (i.e. R_{C18:0/oleic acid} - Δ9-desaturase index) in the liver of rats fed the experimental diets increased.