The aim of the study was to determine the influence of diets containing 1.5% conjugated linoleic acid isomers (CLAmix) and/or a high or low level of selenite (0.2 ppm Se (_LSe) or 0.5 ppm Se (_HSe)) on the body weight gain (BWG), feed conversion efficiency (FCE), and concentrations of CLA isomers and other fatty acids (FA) in the liver and femoral muscle of female rats fed ad libitum these experimental diets for 6 weeks. It was found that the diet containing the CLAmix and 0.5 ppm Se (_HSe) resulted in the highest increase in BWG and FCE compared with values for BWG and FCE of all other groups. This diet most efficiently increased the concentration of Se in the liver and muscles. The content of CLA isomers in muscles was ~20-fold higher than in the liver. There were usually no differences in the concentrations of c9t11CLA, t10c12CLA and the sum of CLA isomers in the liver and muscles of rats fed the diet with CLAmix with or without _HSe, whereas these values in the liver and muscles were usually lower for rats fed the diet enriched in CLAmix and 0.2 ppm Se (_LSe) compared with those fed the diet with CLAmix. The diets enriched in CLAmix and/or Se (as _LSe or _HSe) caused a decrease in the Δ9-desaturase index only in the liver. The current study shows that the highest values of the Δ4-, Δ5- and Δ6-desaturase indexes were in muscles of rats fed the diet enriched in CLAmix. This diet most efficiently increased the value of the Δ4-desaturase index in the liver, the desaturase responsible for the most efficient increase in the content of c4c7c10c13c16c19C22:6n-3 in the liver. Our study indicates that dietary CLAmix stimulated β-oxidation of FA in skeletal muscles, while promoting the accumulation of FA, particularly n-3 polyunsaturated fatty acids (PUFA), in the liver. The diet enriched in CLAmix and _HSe assured satisfactory ratios of PUFA to saturated FA and PUFA to the sum of all assayed FA in the liver and muscles. These findings are valuable information for nutritionists carrying out research to improve the nutritive value of food for human health. Further studies are necessary to thoroughly investigate the effects of dietary CLA isomers as well as interactions of CLA isomers and Se compounds on the human health.