In metabolic animal models, researchers often use male rodents because they show metabolic disease better than females. Thus, females are underrepresented in these studies because of an acknowledged sex difference. In this perspective article, F. Mauvais-Jarvis and colleagues discuss the experimental design and interpretation of studies addressing the mechanisms of sex differences in metabolic homeostasis and disease, using animal models and cells. The authors also highlight current limitations in research tools and attitudes that threaten to delay progress in studies of sex differences in basic animal research.