The purpose of the investigation was to determine the short-term influence of the addition of linseed oil (LO) and Se as selenate (SeVI) on the concentration of fatty acids (FA), especially conjugated linoleic acid (CLA) isomers, in the spleen, pancreas, and kidneys of lambs. The experiment was carried out on 20 lambs (25±2 kg) allotted to 4 groups of 5 animals each. For 35 days the lambs were fed a basal diet composed of concentrate and hay (control group; C) or supplemented with: 5% linseed oil (group LO), 2 ppm Se as SeVI (group SE); combined addition of LO and SeVI (group LOSE). The results showed that short-term feeding of lambs with the diet enriched with LO, irrespective of the presence of SeVI, increased body weight gain and feed conversion efficiency compared with the control and SE groups. Feeding LO and SeVI most effectively stimulated the accumulation of Se in the spleen and pancreas. The diet with LO most efficiently increased the level of cis9trans11CLA (c9t11CLA), the sum of ct/tcCLA, ttCLA, all CLA isomers, and FA containing conjugated double bonds in the spleen and pancreas. The c9t11CLA/t10c12CLA ratio was highest in all assayed organs of lambs fed the diet with SeVI. The diet with LO, irrespective of the presence of SeVI, increased the concentration sum of monounsaturated FA and all FA in all organs compared with the C and SE groups. The LO and LOSE treatments decreased the values of the atherogenic and thrombogenic indexes in the spleen and pancreas compared with the control and SE groups and increased the concentration of polyunsaturated FA in all organs as compared with the same groups. Feeding lambs the diet enriched in LO or SeVI increased the value of the Δ9-desaturase index in the pancreas compared with the control and LOSE groups, while decreased values of this index were found in the spleen and kidneys of lambs fed the LO, SE, or LOSE diet. Our results of feeding diets with LO and SeVI constitute useful information for nutritionists carrying out further investigations to improve performance and the nutritional quality of feed for ruminants.