A 2 × 3 factorial study was conducted to evaluate the effects of dietary lipid level on mitochondrial gene expression in mixed sex rainbow trout Oncorhynchus mykiss. Practical diets with a fixed crude protein content of 42%, formulated to contain 10% (42/10), 20% (42/20) and 30% (42/30) dietary lipid, were fed to triplicate groups of either low-feed efficient (F129; mean ± s.d. = 105.67 ± 3.04 g initial average mass) or high-feed efficient (F134; mean ± s.d. = 97.86 ± 4.02 g) families of fish, to apparent satiety, twice per day, for 108 days. At the end of the experiment, diets 42/20 and 42/30 led to similar fish condition factors, which were higher than that observed with diet 42/10 (P < 0.05). F134 fish fed diet 42/10 showed the highest hepato-somatic index, while there was no significant difference among all the other treatments (P < 0.05). When the group of F134 fish fed diet 42/10 was used as the calibrator for gene expression analysis, the five genes selected for their involvement in lipid metabolism (complex I-nd1, complex III-cytb, complex IV-cox1, complex IV-cox2 and complex V-atp6) were up-regulated in the muscle and down-regulated in both the liver and the intestine. There was a significant family × diet interaction regarding nd1, cox2 and atp6 in the liver; nd1, cytb, cox1, cox2 and atp6 in the intestine, and nd1, cytb, cox1, cox2 and atp6 in the muscle (P < 0.05). The overall results of this study constitute basic information for the understanding of molecular mechanisms of lipid metabolism at the mitochondrial level in fishes.