To investigate the effect of dietary protein sources on gene expression of proteins involved in the regulation of lipid, glucose and energy metabolism in white and brown adipose tissues and skeletal muscle, male ICR mice were fed an experimental diet containing either casein, soybean protein or whole egg protein for 21 days. The serum glucose level was significantly higher in mice fed whole egg protein than in the other groups. However, no protein-dependent changes were seen in serum lipid levels. Compared to casein and soybean protein, whole egg protein significantly decreased glucose transporter 4 mRNA abundance in perirenal white adipose tissue and interscapular brown adipose tissue. Uncoupling protein 2 mRNA level in perirenal white adipose tissue and brown adipose tissue was significantly higher in mice fed soybean protein than in those fed casein. Compared to other protein sources, whole egg protein increased uncoupling protein 2 mRNA level in skeletal muscle. Whole egg protein, compared to other proteins, significantly increased the hepatic peroxosimal fatty acid oxidation rate. However, mitochondrial fatty acid oxidation rate was the lowest in mice fed whole egg protein among the animals fed different proteins.