The influence of 1.2 ppm dietary selenium added in the form of selenized yeast (Se-yeast) and of a mixture of conjugated linoleic acid (CLA) isomers added to a level of 1 or 2%, of cis9trans11CLA (c9t11) added to 1%, and of trans10cis12CLA (t10c12) added to 1% on the body and organ gains of rats and on the concentration of CLA isomers and other fatty acids in the spleen, pancreas and kidneys was investigated. Total fatty acids in the studied organs were separated as methyl esters using long-capillary gas-liquid chromatography with flame-ionization detection, while nonmethylated fatty acids containing conjugated double bonds were examined using silver-ion liquid chromatography with fotodiode detection. Free fatty acids were obtained by mild saponification, whereas their methyl esters, by base- and acid-catalyzed methylation. Feeding t10c12 and Se-yeast resulted in the highest increase in rat growth and organ gain. All diets enriched in CLA isomer(s) significantly elevated the concentration of CLA isomers in the organs; the highest concentration of CLA isomers was found in the pancreas, the smallest, in the spleen. The addition of Se to diets containing CLA isomer(s) usually showed a statistical tendency or increase in the concentration of CLA isomers in the organs. Our results demonstrate that t10c12 was metabolized faster than c9t11 in the pancreas and kidneys, whereas the addition of Se-yeast to the diets with CLA isomer(s) reduced the rate of t10c12 metabolism. A 2% dietary content of a mixture of CLA isomers or of t10c12 usually tended to increase or significantly increased the concentration of linoleic, linolenic, and arachidonic acids and of n-3 long-chain polyunsaturated fatty acids (n-3 PUFA) in the organs. Dietary c9t11 and a 1% content of the mixture of CLA isomers weakly influenced the concentrations of these fatty acids in the organs, whereas the diet enriched simultaneously in c9t11 and Se-yeast resulted in a statistical tendency or increase in the concentration of long-chain n-3 PUFA and the sum of PUFA in the organs compared with the control group and rats fed the diet containing only c9t11. The obtained results suggest that t10c12 and, in particular, 2% of the mixture of CLA isomers decreased the capacities of Δ9-, Δ6-, Δ5- and Δ4-desaturases, as well as of cyclooxygenase-1, and/or the inducible form, cyclooxygenase-2, at the level of mRNA, protein, or activity.