Intra-specific variation in basal metabolic rate (BMR) has profound evolutionary, ecological, and biomedical consequences. However, functional mechanisms responsible for this variation are still not fully understood. Theoretically, variation in BMR can reflect differences in either the mass of internal organs, and/or in the rate of organ mass-specific metabolic processes. Here, we compared parameters quantifying mitochondrial metabolic activity in two lines of laboratory mice, divergently selected for either high (H-BMR) or low (L-BMR) level of BMR. H-BMR mice had larger liver and kidneys, i.e. organs that are important predictors of BMR. On the other hand, our preliminary data offer little evidence that selection affected intrinsic properties of mitochondria like mitochondrial activity and efficiency, or activity of mitochondrial enzymes like citrate synthase and cytochrome c oxidase. We conclude that variation in BMR observed between both selected lines reflects mainly changes in organ size rather than in mitochondrial-specific metabolic rate. These results, together with earlier analyses of cell membrane composition, suggest that divergent selection for BMR either did not affect metabolic parameters at molecular level or modified them in counter-intuitive direction. We discuss other potential mechanisms of difference in BMR between these lines.