Polyunsaturated omega-3 fatty acids (n-3 PUFAs) have been suggested to reduce risk for multiple diseases but animal studies on the beneficial effects of n-3 PUFAs are conflicting, possibly due to the presence of toxic lipid oxidation products in the oils used in these studies. In order to provide guidance for future research in n-3 PUFA supplementation, this study researched lipid oxidation and its inhibition in an animal feed system enriched with fish oil. Different storage conditions were tested, and it was found that samples stored at room temperature or above were at significant risk for oxidation with lag phases of propanal formation being 56, 8 and 2 days at 4°C, 23°C and 37°C. More than 65% removal of oxygen was needed to significantly decrease lipid oxidation. Greater than 65% removal of oxygen could be achieved in less than 1 minute of nitrogen flushing. Tocopherols were not strong antioxidants in the animal feed but Trolox was, suggesting that the fish oil enriched rodent feed acts similarly to bulk oil. Both ascorbic acid and ascorbyl palmitate were found to be ineffective, possibly due to their prooxidant activity. In a comparison of propyl gallate (PG), butylhydroxy toluene (BHT), and tert-butylhydroquinone (TBHQ), results were found similar to other low-moisture systems, with PG being prooxidative, BHT improving lag phase, and TBHQ having a significant impact on lag phase. These results suggest that lipid oxidation products can be present at the start of a dietary omega-3 fatty acid study if poor quality oils are used and that oxidation can occur in the feed during storage times common to animal studies. These findings indicate that researchers should use antioxidant strategies to control oxidation in animal feeds to avoid potentially conflicting effects of lipid oxidation products in dietary omega-3 fatty acid studies.