The influence of diets enriched in 2% CLA isomer mixture (as CLAmix_A or CLAmix_B) and/or Se as selenate (Se^VI) or selenized yeast (Se-Y) on the concentration of fatty acids (FA) and amino acids (AA) in the liver and femoral muscles was studied on 8 groups of 7-8 rats aged 8 weeks. Rats were fed a basal diet for 29 days or diets enriched with two combinations of 2% CLAmix_A with/without 2 ppm Se (as Se^VI) or 2% CLAmix_B with/without 1.2 ppm Se (as Se-Y). The dietary CLAmix_B containing the higher concentration of trans10cis12CLA (t10c12CLA) resulted in a higher decrease of body weight gain (BWG) (P<0.1) than the dietary CLAmix_A with the lower concentration of t10c12CLA. The diet enriched in Se^VI reduced the BWG (P<0.05) in rats. The dietary CLAmix_A lowered the concentration of saturated FA (SFA), atherogenic SFA and thrombogenic SFA in the liver and muscles. The value of the Δ9-desaturase index decreased in the liver and muscles of rats fed the diet enriched in CLAmix _A or CLAmix_B compared with that in the control rats. There were significantly higher (P<0.01) concentrations of c9t11CLA, t10c12CLA, ccCLA and ttCLA in the muscles compared with the concentrations of these isomers in the liver of rats fed the diets enriched in CLAmix _A or CLAmix _B, regardless the presence of extra Se as Se^VI or Se-Y. The ratio (R_t10c12/c9t11) of t10c12CLA and c9t11CLA in the liver and muscles of rats fed the diets enriched in CLA isomers was, regardless of the presence of Se, smaller compared with the values of R_t10c12/c9t11 in the dietary CLA isomers. The concentrations of CLA isomers tended to or significantly increased in the liver and muscles of rats fed diets containing Se and CLA isomers compared with rats fed the diets enriched in CLA isomers. The concentrations of PUFAn-3, PUFAn-6, PUFA and the ratio of PUFA/SFA decreased in the muscles of rats fed the diet with CLAmix _A. The results suggest that the dietary CLAmix_A containing the higher concentration of ttCLA, regardless of the presence of Se^VI, more efficiently reduced the magnitude of lipoprotein synthesis in muscles than the diet containing CLAmix_B with/without Se-Y, while dietary Se-Y most effectively reduced the anti-obesity properties of CLA isomers in rats. The diets enriched in CLA isomers (as CLAmix_A or CLAmix_B), regardless of the presence of Se^VI, led to a decrease in the concentration of methionine (Met) in the liver and the concentration of all amino acids in the muscles, while increasing the concentration of Met in muscles.