The intestinal absorption of omega-3 long chain polyunsaturated fatty acids (ω3 LCPUFA), [eicosapentaenoic acid (EPA) + docosahexaenoic acid (DHA)], after consuming fish oil gelatine capsules or different food products fortified with microencapsulated fish oil, was determined using human ileostomates. The total amount of ω3 LCPUFA consumed per dose of fish oil capsule was 266 mg while that for fortified orange juice, yoghurt and cereal bar was 284 mg per serving of food product. In a time course experiment ω3 LCPUFA was measured in ileal effluent over 24 h post ingestion. Only 0.58–0.73% of the total ω3 LCPUFA dose was recovered in the ileal effluent irrespective of whether the fish oil was delivered in a gelatine capsule or in the form of a microencapsulated powder incorporated into fortified foods. Excretion of ω3 LCPUFA was detected in the 2–18 h effluent collections with none detected at 0 h or 24 h. post ingestion. The transit time of the minimal amount of ω3 LCPUFA that remained in the ileal effluent was dependent on the method of delivery of the fish oil. The ω3 LCPUFA content in the ileal effluent peaked at 2–8 h and declined after 10 h after consumption of fish oil capsules and fortified orange juice. In contrast, two peaks in ω3 LCPUFA content were observed in the ileal effluent, first at 2–8 h and again at 14–16 h, after consumption of fortified yoghurt and cereal bar. The highest recovery of the small amount of ω3 LCPUFA in the ileal effluent at 14–16 h was obtained when fortified cereal bar was consumed. The results suggest that the delivery of fish oil through food products fortified with microencapsulated fish oil does not compromise the bioavailability of the ω3 LCPUFA as evidence by no statistical differences detected in the remaining portion of ω3 LCPUFA in the ileal effluent (p = 0.58). However, the food matrix in which the microencapsulated oil was delivered may alter the transit kinetics of the ω3 LCPUFA through the small intestine.