The aim of the study was to determine the influence of conjugated isomers of linoleic acid (CLA) and/or selenium (Se) on the body mass gain of rats, feed intake, and the levels of CLA isomers and some other fatty acids in the femoral muscle. Rat diets enriched in Se, the trans-10,cis-12 isomer and mixtures of the CLA isomers (regardless Se supplementation) tended to decrease body mass gain compared with control rats, while simultaneously supplementation with Se and the trans-10,cis-12 isomer resulted in the highest increase. A mixture of CLA isomers and/or Se supplementation, and the trans-10,cis-12 isomer decreased feed intake, whereas the cis-9,trans-11 isomer, regardless of Se supplementation, only slightly influence of feed intake. Enriching diets with CLA isomers increased their level in muscles as well as the level of non-CLA isomers containing conjugated double bonds (CD). In rats receiving simultaneously Se and mixtures of the CLA isomers or individual CLA isomers the CLA isomers and CD levels in muscles were higher compared with rats fed only the CLA isomers. Rats fed individual isomers or their mixture showed minute changes in C8:0 and C10:0 concentrations in muscles, while the C12:0, C14:0, C16:0 and C18:0 contents were generally lower. A small increase in C10:0 and C16:0 content was found in rats fed the trans-10,cis-12 isomer. Supplementing Se to diets enriched in CLA isomers usually resulted in an increase in the saturated fatty acid content in muscles in comparison with rats fed only CLA isomers. The linoleic acid content in muscles was enhanced by the Se supplemented diets enriched in the trans-10,cis-12 isomer or in the 2% CLA isomer mixture, although 1% mixture of the CLA isomers or the cis-9,trans-11 isomer dosed simultaneously with Se also increased the level of linoleic acid, albeit insignificantly. The Se supplemented diet enriched in the trans-10,cis-12 isomer or 2% mixture of the CLA isomers produced the highest increase of γ-linolenic acid, the total fatty acid and polyunsaturated fatty acid content in rat muscle.