Oxidation of cod liver oil rich in long-chain n-3 polyunsaturated fatty acids (LC n-3 PUFA) was investigated during a gastrointestinal (GI) in vitro digestion. The digestion stimulated TBA-reactive substances (TBARS) formation in both the gastric and intestinal steps, whereas levels of lipid hydroperoxides remained nearly constant. The presence of digestive compounds was decisive for the TBARS development because TBARS did not change when the cod liver oil was subjected only to the temperature and pH gradient of the GI model. Preformed oxidation products in the cod liver oil resulted in further elevated TBARS levels during the digestion. Addition of hemoglobin (11.5 μM) to emulsified cod liver oil dramatically increased TBARS and lipid hydroperoxide levels during GI digestion, whereas 1 mg α-tocopherol/g oil did not show any protection against oxidation. Specific concern thus needs to be taken in the design of foods containing LC n-3 PUFA to preserve these lipids and avoid harmful oxidation, both before and after consumption.