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Summary Background & aims The importance of route of administration of omega-3 (n-3) polyunsaturated fatty acids (PUFA) (oral vs intravenous (iv)) is not clear. We determined the relative concentrations of fatty acids in plasma phosphatidylcholine (PC), red blood cells (RBC), white blood cells (WBC) and several tissues after short-term oral or iv administration of soybean oil (SO) or fish oil (FO). Methods Wistar rats ( n = 6/group) received saline, FO, or SO by gavage or saline, FO based-lipid emulsion (FLE), or SO based-lipid emulsion (SLE) iv. The oils were provided at 0.2 g/kg/day for three consecutive days. The animals were sacrificed 24 h after the last administration, blood was collected for plasma, WBC and RBC separation and tissues removed. Fatty acids were analysed by gas chromatography. Results FO resulted in higher eicosapentaenoic acid (EPA) in plasma PC and liver than the control. FLE resulted in higher EPA, docosahexaenoic acid (DHA) and total n-3 PUFA in plasma PC, WBC and liver than both the control and SLE groups. EPA, DHA and total n-3 PUFA were higher in the heart with FLE compared with SLE. Individual and total n-3 PUFA were higher in plasma PC, WBC, liver and heart with FLE than with FO given by gavage. Conclusion Short-term iv administration of n-3 PUFA appears to be more effective at increasing EPA and DHA status in plasma, WBC, liver and heart than oral administration. This might be important for rapid treatment with n-3 PUFA.