The main objective of this study was to evaluate the influence of diets enriched in individual conjugated linoleic acid (CLA) isomers, their mixture, and/or selenized yeast (Se-yeast) on the concentration of CLA isomers, long-chain polyunsaturated fatty acids (PUFA) and Se in the heart, muscles and liver of rats. The investigation was performed on 73 female Wistar rats (8 weeks of age, 200 g initial BW). After one week sub-maintenance feeding, rats received diets supplemented with 1% individual CLA isomers or 1 or 2% of a CLA isomers mixture, without or with 1.2 mg Se/kg (as Se-yeast) for 29 days. Feeding diets with 2% CLA isomer mixture reduced feed intake and body weight gain of rats, while addition of trans10,cis12 CLA and Se-yeast resulted in the highest body weight gain. CLA supplementation generally elevated the concentration of CLA isomers in heart and muscles significantly, although cis9,trans11 CLA accumulated preferentially. Regardless of the presence of Se-yeast, the dietary enrichment with CLA isomers caused a reduction in the capacity of A9-desaturase. Addition of Se-yeast to diets with individual CLA isomers or a 1% mixture of CLA isomers elevated the accumulation of CLA isomers in the heart and muscles, whereas all treatments with supplemented CLA and Se-yeast increased the accumulation of Se in rats compared with animals fed the diet containing Se only. Furthermore, CLA isomer supplementation decreased the concentration of PUFA and total fatty acids in the heart and muscles compared with control rats. Moreover, addition of CLA isomers interfered in the conversion of linoleic and linolenic acids to higher metabolites due to competition of CLA isomers for the same enzymes (delta6-, delta5-, delta4-desaturases and elongase).