The objective of this study was to determine the conjugated linoleic acid (CLA) isomer composition of blood plasma and other organ tissues of Wistar rats fed a diet enriched with 1 or 2% CLA isomer(s) and 2 ppm Se as sodium selenate for 4 weeks. The dietary supplement of CLA isomers significantly elevated the concentration of CLA isomers and other fatty acids containing conjugated double bonds in plasma, spleen, pancreas, heart, and kidney tissues. cis9,trans11CLA was preferentially accumulated in plasma and organ tissues of rats fed the CLA isomer mixture with or without Se, while the percentage contribution of trans10,cis12CLA in the tissues of organs tended to be lower than its percentage in the administered CLA isomer mixture. Dietary CLA isomer(s) increased the Ca content of whole blood, while the diet with the CLA isomer(s) and Se increased the concentration of Mg and Se in spleen tissue. The experimental diets did not produce any substantial changes in the Fe or Zn concentrations in blood or spleen tissue. The diet enriched in trans10,cis12CLA and Se significantly increased spleen, pancreas and heart weights. Regardless of the presence of Se, the diet enriched in CLA isomer(s) stimulated the accumulation of polyunsaturated fatty acids in blood plasma, and in pancreas, heart, and kidney tissues. The diets enriched in the CLA isomer(s) usually resulted in a decrease of the monounsaturated fatty acid concentration and Δ9-desaturase capacity in plasma, spleen, pancreas, and kidney tissues, but not in noticeably decreased concentrations in heart and brain tissues. The presence of both Se and the CLA isomer(s) produced less consistent changes in the capacity of Δ9 desaturase and monounsaturated fatty acid concentrations compared with the effect of the diet with the CLA isomer(s) only.