Abstract The aim of this study was to examine the effects of n-3 polyunsaturated fatty acids (PUFAs) of different marine origins on the metabolism of chylomicrons following a single ingestion of oil. Two oils both rich in n-3 PUFAs but differing with respect to the intramolecular structure of the triglycerides (TGs) were compared, the first a fish oil with the sn-2 position of TGs enriched with n-3 PUFAs and the second a seal oil with the n-3 PUFAs located in the sn-1/3 positions of the TGs. Radiolabeled rat mesenteric lymph chylomicrons were prepared following intragastric administration of the respective oil in which [ 3H]-cholesterol and [ 14C]-palmitic acid were dissolved to label the lymph chylomicrons cholesterol and triglycerides, respectively. After intravenous injection of chylomicrons into unanesthetized rats, removal from plasma of radiolabeled cholesterol and palmitate, and uptakes of radiolabels by the liver and spleen were measured. The disappearance of cholesterol label was faster following injection of seal oil chylomicrons compared with fish oil chylomicrons whereas there were no differences in the disappearance of palmitate label. The recovery of palmitate label in the liver after 30 min was significantly higher following injection of fish oil chylomicrons compared with seal oil chylomicrons. Our data demonstrate that the metabolism of chylomicrons is affected by the intramolecular structure of the TG in the dietary oils rich in n-3 PUFAs but the mechanism by which the metabolism is affected is yet unknown.