The influence of diets enriched in CLA isomers and/or selenium on the concentration of fatty acids and amino acids in blood plasma was studied on 20 groups of 7-8 rats aged 8 weeks and with a body weight (BW) of about 201 g. Rats were fed a basal diet for 29 days or a diet enriched with a combination of 1 or 2% CLA isomer(s) and/or 2 ppm as selenate, 1.2% as selenized yeast. Diets enriched in 1% of t10c12CLA and Se compounds caused the most efficient body weight gain (BWG) and feed conversion. Diets enriched in Se compounds only showed a tendency to decrease BWG and feed conversion efficiency compared with control rats. Diets with CLA isomers increased isomer concentrations in plasma with preferential accumulation c9t11CLA in comparison with t10c12CLA. Supplemental Se and CLA isomer mixture usually increased β-oxidation of t10c12CLA compared with supplementing the CLA isomer mixture only. Supplementing 1% of the CLA isomer mixture showed tendency to decrease the concentration of C16:0 and SFA in plasma but supplementing 1 or 2% of the isomer mixture with Se compounds tended to or significantly decreased C16:0 and SFA in plasma. The t10c12CLA isomer reduced, whereas c9t11CLA, stimulated the yield of Δ9-desaturation. An increase of linoleic and linolenic acid concentrations was found in the plasma of rats fed the diet with CLA isomer(s) and Se sources compared with the control diet. Supplementing Se sources or CLA isomer(s) stimulated MUFA and PUFA accumulation in plasma due to stimulation of Δ9-, Δ6- and Δ4-desaturation and elongation of fatty acids. Supplementing CLA isomers increased the concentration of amino acids in plasma, while the interaction between supplemented c9t11CLA and t10c12CLA in rats resulted in reduction of the concentration of amino acids in plasma.