The effects of conjugated linoleic acid (CLA) isomers and/or selenium (as Na₂SeO₄) on rat growth performance and levels of some fatty acids (FA) in femoral muscles and perigonadal fat were investigated. Feeding a mixture of CLA isomers, the trans-10,cis-12 isomer, or selenium (Se) tended to decrease the rats’ body weight compared with the control animals, whereas a diet supplemented with both Se and the trans-10,cis-12 isomer produced the highest increase in body weight gain and the highest feed conversion efficiency. None of the experimental diets had any influence on brain, kidney, pancreas, or liver weight, while they significantly increased spleen mass. The administered CLA isomers significantly increased the contents of CLA isomers and non-CLA fatty acids containing conjugated double bonds (CD) in the assayed tissues. Se and individual CLA isomers or their mixture increased the CLA isomer and CD contents in muscles, while feeding only the cis-9, trans-11 isomer and Se resulted in an increase in CD and sum of all CLA isomers in fat. These results demonstrate that the trans-10,cis-12 isomer is preferentially driven through the β-oxidation pathway in muscles and fat compared with the cis-9,trans-11 isomer. CLA isomers added to Se-unsupplemented or -supplemented diets increased the levels of total FA in muscles only, while decreased the level of total assayed saturated FA in fat. Feeding Se and individual CLAs or a mixture of these isomers resulted in increasing both the sum of cis-monounsaturated FA (cis-MUFA), CD and polyunsaturated FA (PUFA) in muscles, but generally resulted in decreasing the level of total saturated FA, cis-MUFA and PUFA in fat. The interaction between Se and a mixture of CLA isomers or the trans-10,cis-12 isomer most effectively protected CLA isomers from peroxidation damage and/or catabolism in muscles.