Nutritional and biochemical properties of noncommercial whey protein have been described since 1950. However, comparisons between commercial whey protein for human consumption and casein are rarely found. The aim of this study was to compare biological quality of a commercial whey protein with casein and its effect on biochemical parameters of rats. Thirty-two weanling Fisher rats were divided into three groups and given the following diets: casein group, standard diet (AOAC); whey protein group, modified AOAC diet with whey protein instead of casein; and casein:whey group, modified AOAC diet with 70%:30% casein:whey. A protein-free group was used for determination of endogenous nitrogen losses. Net protein ratio, protein efficiency ratio, and true digestibility were determined, and blood was collected for biochemical analysis. When compared with casein, whey protein showed significant differences for all biological parameters evaluated, as well as for albumin, total protein, total cholesterol, and glucose concentrations. Replacing 30% of casein with whey protein did not affect these parameters. A positive relation among whey protein, high-density lipoprotein-cholesterol, and paraoxonase activity was found. Hepatic or renal dysfunctions were not observed. In conclusion, in comparison with casein, commercial whey protein had higher values of biological parameters, and biochemical evaluation revealed it improved glycemic homeostasis, lipid status, and paraoxonase activity in rats.