Sex differences are described in subregions of two nuclei of the rat brain: the medical nucleus of the amygdala (MA) and the bed nucleus of the stria terminalis (BNST). The volume of the posterodorsal region of the medial nucleus of the amygdala (MApd) is approximately 85% greater and the volume of the encapsulated region of the bed nucleus of the stria terminalis (BNSTenc) is approximately 97% greater in males than in females. The MApd and BNSTenc are distinct subregions of the MA and BNST. They exhibit intense uptake of gonadal hormones and are anatomically connected to each other and to other sexually dimorphic nuclei. The MA and BNST in general are involved in regulation of several sexually dimorphic functions, including aggression, sexual behavior, gonadotropin secretion and integration of olfactory information. Precise localization of sex differences in subregions of the MA and BNST, such as the MApd and BNSTenc, may facilitate understanding of the neural basis of such functions.