An average recovery of 57.7% is obtained when cultured yellowtail are processed into fillets, while the remaining 42.3% forms wastes, primarily composed of heads, backbones, and viscera. The head, accounting for 13.8%, contained high levels of lipid, making it a suitable source for recovering EPA and DHA for food application. The lipid was tested to supplement to jyakotenpura, a special kamaboko of Ehime, and was added to chicken feed to enrich DHA in an egg yolk. Cultured yellowtail backbone (8.7% of the round fish) contained relatively high levels of lipid. When the bones were retorted, they turned to edible products due to fragility induced by gelatinization of bone matrix collagen. The retorted bones were easily crushed into fine paste-like homogenates, which were utilized as functional additives to various types of kamaboko, seasoning, and soup stock to enrich EPA, DHA, and minerals. The retorted bone was superior as a source of calcium to chemicals, such as CaPO3, because of a low interference of iron absorptivity.