The discarded internal organs of the Japanese giant scallop (Patinopecten yessoensis) are abundant resources rich in n-3 polyunsaturated fatty acids (PUFA), such as eicosapentaenoic acid and docosahexaenoic acid. However, they have not been utilized due to contamination with toxic substances such as cadmium (Cd) and the occurrence of diarrhetic shellfish toxins (DST). We have successfully prepared a high-quality scallop oil (SCO) from its internal organs with negligible contamination with Cd and DST. The scallop internal organs were obtained from two different scallop processing areas, Mutsu and Uchiura bays, Japan, and referred to as SCO-M and SCO-U, respectively. To evaluate the safeties of SCO-M and SCO-U as food ingredients and n-3 PUFA supplements, repeated 28-day and 13-week dose oral toxicity studies in rats were conducted. Rats were fed diets containing 1% and 5% of SCO-M and SCO-U, respectively, in the repeated 28-day dose oral toxicity study and 5% SCO-M or SCO-U in the repeated 13-week dose oral toxicity study (limit test). No adverse toxicological effects were observed when rats were fed diets containing SCO-M and/or SCO-U at up to 5% for 28 days and 13 weeks. These results suggest that SCO-M and SCO-U are safe products in terms of subacute toxicity under these experimental conditions.