We examine variation associated with phylogeny in the scaling of body temperature in endotherms, using data from 596 species of mammal and 490 species of bird. Among higher groups of mammals there is statistically significant scaling of body temperature with mass in Marsupialia (positive), Ferae and Ungulata (both negative). In mammalian orders where data are available for at least 10 species, scaling is negative in three orders (Carnivora, Erinaceomorpha and Artiodactyla), positive in one (Chiroptera) and not significant in seven others. There is no relationship apparent between the scaling of body temperature and the existence of gut fermentation. As expected, monotremes exhibit the lowest body temperatures, but within marsupials diprotodonts have a mean body temperature higher than several placental groups; the traditional ranking of body temperatures in the sequence monotremes – marsupials – placentals is thus misleading. In birds, scaling relationships are significant only for Ciconiiformes (strongly negative) and Passeriformes (weakly positive). When allowance is made for phylogenetic effects, there is no significant relationship between temperature in body mass in mammals overall, but an inverse and almost significant relationship in birds. This study indicates a complex relationship between body mass, body temperature and metabolic rate in mammals and birds, mediated through ecology.