Objectives <p>Basal metabolic rate (BMR) and body temperature are evolutionarily coupled in mammals. Low values of both BMR and body temperature, and high lability (instability) of body temperature in response to unfavorable conditions are important predictors of obesity risk. Therefore, clarifying their mutual dependencies is important for interpreting the results of translational studies. The aim of our study was to determine how large intraspecific variation in BMR affects body temperature and its lability in laboratory rodents with different levels of obesity.</p> Methods <p>We measured core body temperature by means of implanted loggers in males from two lines of laboratory mice divergently selected for high (H-BMR) or low (L-BMR) BMR and acclimated to 23 °C and 4 °C.</p> Results <p>The relative between-line difference in BMR reached 60%. H-BMR males had a 0.32 °C higher mean body temperature than L-BMR males at 23 °C, but this difference was not significant at 4 °C. The effect of selection on mean body temperature was weaker than that on BMR and daily energy expenditure. Acclimation to 4 °C decreased body temperature more in H-BMR males than L-BMR males, but this effect resulted from lower nighttime (i.e., active phase) body temperature in this line, presumably reflecting greater heat loss due to elevated locomotor activity.</p> Conclusions <p>We conclude that the large intraspecific variation in BMR in laboratory mice can be accompanied by significant variation in mean body temperature. However, the flexibility of the energy budget (e.g., changes in the magnitude of dedicated thermogenesis or in locomotor activity) can sometimes attenuate the correlation between BMR and body temperature. As a consequence, in the studied lines, BMR is a better predictor of fat content than body temperature and its lability. Thus, all studies of the link between body temperature and other traits like obesity should take into account variation in BMR.</p>