We investigated strain differences in whole body energy metabolism, peripheral lipid metabolism, and energy metabolism-related gene expression and protein levels in BALB/c, C57BL/6J, and A/J mice to evaluate the relationship between endurance capacity, susceptibility to diet-induced obesity, and differences in lipid metabolism in muscle and liver. A high-fat diet significantly increased body weight and fat weight in C57BL/6J mice, but not in BALB/c and A/J mice. The endurance capacity of BALB/c mice was 52% greater than that of C57BL/6J mice and 217% greater than that of A/J mice. The respiratory exchange ratio was lowest in BALB/c mice, higher in C57BL/6J mice, and highest in A/J mice, which inversely correlated with the endurance capacity and fatty acid beta-oxidation activity in the muscle. Plasma lactate levels measured immediately after exercise were lowest in BALB/c mice and highest in A/J mice, although there was no difference under resting conditions, suggesting that carbohydrate breakdown is suppressed by enhanced fat utilization during exercise in BALB/c mice. On the other hand, the body weight increase induced by high-fat feeding was related to a reduced whole body energy expenditure, higher respiratory quotient, and lower fatty acid beta-oxidation activity in the liver. In addition, beta-oxidation activity in the muscle and liver roughly paralleled the mRNA and protein levels of lipid metabolism-related molecules, such as peroxisome proliferator-activated receptor and medium-chain acyl-CoA dehydrogenase, in each tissue. These findings indicate that genetically determined basal muscle and liver lipid metabolism and responsiveness to exercise influence physical performance and obesity susceptibility.