Phenotypic variation in physiological traits, such as energy metabolism, is commonly subjected to adaptive interpretations, but little is known about the heritable basis or genetic correlations among physiological traits in non-domesticated species. Basal metabolic rate (BMR) and body mass are related in complex ways. We studied the quantitative genetics of BMR, residual BMR (on body mass), mass-specific BMR and body mass of stonechats originating from four different populations and bred in captivity. Heritabilities ranged from 0.2 to 0.7. The genetic variance–covariance structure implied that BMR, mass-specific BMR and body mass can in part evolve independently of each other, because we found genetic correlations deviating significantly from one and minus one. BMR, mass-specific BMR and body mass further differed among populations at the phenotypic level; differences in the genetic correlation among populations are discussed.