Yellowtail kingfish (Seriola lalandi) is a valuable commercial aquacultural product in high demand in several countries. Growth performance, survival, lipid content, antioxidant enzyme system defense, gene expression and malformation were investigated in the juvenile specimens subjected to different diets. Three experimental diets with different proportions of fish oil (FO) and olive oil (OO) and different levels of long chain polyunsaturated fatty acids (LC PUFA), were formulated and manufactured: D1: 100% FO + 0% OO; D2: 50% FO + 50% OO; D3: 0% FO + 100% OO. S. lalandi juveniles weighing 0.81 g (57 days dph) were fed during four weeks with experimental diets (D1, D2, and D3). Samples of normal or malformed-jaw fish were collected at the end of the feeding trial. Although the incidence of malformations seemed to slightly increase with the incorporation of OO, the statistical association between diet and the malformation rate was not clear. The most frequent malformation observed was shortening of the lower jaw, followed by shortening of the upper jaw. At the gene expression level, the antioxidant genes CAT, SOD, GPX, RXR and PPAR were upregulated in malformed-jaw fish compared to normal specimens, independent of their diets. The results of multi-dimensional scaling suggest that a disruption of hepatic lipid composition may be associated with jaw and operculum malformations in juvenile S. lalandi.