In this study we report that, unlike the case of obese or high-fat fed animals, consumption of a whey protein hydrolyzate can have a minimal impact on skeletal muscle metabolic gene expression in sedentary eutrophic rats and still a moderate effect on body fat. Male Wistar rats were fed diets with either whey-protein concentrate (WPC), a whey-protein hydrolyzate (WPH) or casein (CAS), during two weeks. Gastrocnemius and blood were withdrawn for analysis of the expression of the PPARα, PPARδ, PGC-1α, CPT-1β and myostatin genes, classical serum parameters, non-esterified fatty acids (NEFA), triacylglycerols (TAG), albumin, alanine and aspartate aminotransferases (ALT, AST), in addition to muscle and serum free amino acid profiles. The diet appeared to have no effect on the expression of any of the muscle genes besides, no significant changes being observed in serum NEFA, TAG or creatinine. Compared to CAS, the animals fed either WPC or WPH exhibited lower activities of ALT, AST, together with higher serum albumin levels in the WPC group. It was also observed that the diets containing the whey proteins produced increased levels of serum glycine, whereas in the muscle several amino acids were increased in the animals that consumed WPH. Although the whey protein diets did have an effect on the profile of free muscle amino acids and improved the outcome of classical enzyme biomarkers, consumption did not result in the exacerbation of such parameters of normal animals consuming normolipidic diets.