To better understand intraspecific variation in basal metabolic rate (BMR), we examined environmental, physiological, and/or cellular bases for residual variation in BMR in big brown bats, Eptesicus fuscus. We measured BMR and plasma levels of thyroid hormone (T(3)) and leptin in bats captured in maternity colonies in eastern Massachusetts (MA; northern population) and in Alabama and Georgia (ALGA; southern population) to assess macrogeographic (between- or among-population) and microgeographic (within-population) variation in those traits. After accounting for effects of body mass, stage of pregnancy, and within-population variation, bats from the northern population did not differ significantly in BMR, T(3), or leptin values from those in the southern population. However, after accounting for the effects of body mass and stage of pregnancy, a test for differences in all traits among colonies from both populations was significant. For BMR, bats differed significantly among the northern colonies. Moreover, after removing the effects of body mass and stage of pregnancy, bats from the AL colony had significantly higher BMR than did bats from all other colonies except one in MA, and they had significantly higher T(3) levels but lower leptin levels than did bats from two other colonies. The presence of among-colony and within-population variation for these traits suggests that proximate (nonevolutionary) factors (e.g., microhabitat differences such as roost type) play an important role in shaping intraspecific variation in BMR and its hormone correlates.