The effect of diets enriched in CLA isomer mixture (CLAmix) and/or selenized yeast (Se-Y) on the concentration of fatty acids (FA), amino acids (AA), Se, Fe and Zn in the liver and femoral muscles was studied on 4 groups of 7-8 rats aged 8 weeks. Rats were fed the Labofeed H diet for 29 days (control group) or the diet enriched with 2% CLAmix with or without 1.2 ppm Se as Se-Y (the experimental groups). Feeding the CLAmix-enriched diet reduced the body weight of rats, while the diet containing CLAmix and Se-Y increased it in comparison with the control rats. The muscle concentrations of non-essential and essential amino acids, and in particular, sulphur amino acids (ΣS-AA) can be significantly increased, while the muscle concentration of total fatty acids (ΣFA), decreased by feeding the diet with Se-Y and CLAmix. Feeding the diet with Se-Y leads to significant lowering of the ratios of ΣS-AA, methionine, cysteine and taurine to Se concentrations in the liver and muscles as compared with the control group. Dietary Se-Y or CLAmix lead to a decrease in the concentrations of atherogenic and thrombogenic saturated fatty acids (SFA) in muscles. Feeding the diet with Se-Y and CLAmix increased the concentration of Se and the atherogenic and thrombogenic indexes in the liver and muscles. There were also higher concentrations of cis9trans11CLA and t10c12CLA in the muscles compared with the concentrations of these isomers in the liver of rats fed the diets enriched in only CLAmix. Deposition in the liver and femoral muscle of trans10cis12CLA was higher in both tissues than cis9trans11CLA. The diet with CLAmix, regardless of the presence of Se-Y, decreased the rate of elongation and Δ5-, Δ9-desaturase capacities of in the liver and muscle. The diet with CLAmix effectively increased the ratio of PUFAn-3/SFA, PUFAn-6/SFA, PUFAn-3/ΣFA and PUFAn-6/ΣFA in muscles. The interaction between Se-Y and CLAmix decreased the capacity of liver and muscle desaturation, i.e. these dietary additives reduced the ratio of unsaturated fatty acids to SFA in the liver and muscles.