N-3 polyunsaturated fatty acids from fish oil may have immune-modulating effects in Graft-versus-Host Disease of the digestive tract (GVHD-DT). The objective of this pilot study was to investigate feasibility, safety and effects on fatty acid composition of plasma lipids and white blood cells (WBC), following intermittent fish oil infusion in outpatients with chronic GVHD-DT. Four outpatients received intermittent infusion of a 10% fish oil emulsion (Omegaven) during 4 hours, at day 1 (1.5 mL/kg), 3 (2.25 mL/kg) and 5, 8, 10 and 12 (3 mL/kg). At baseline and consecutive visits, fatty acid composition of plasma triglycerides (TG), plasma phospholipids (PL) and WBC, serum TG concentrations, routine laboratory tests, as well as adverse events were monitored. During the fish oil infusions, serum TG increased, but decreased 2 h after termination of infusion. In 3 patients, the dose of Omegaven ® needed to be reduced. EPA was incorporated into plasma PL, plasma TG and WBC as of 2 days after the first infusion; peak levels of EPA were reached at the final infusion, or 2 days after. In conclusion, intermittent fish oil infusions result in incorporation of EPA in plasma and WBC, but can be complicated by a reversible increase in serum triglycerides.