Laboratory rat strains descend from Wistar rats as a consequence of artificial selection. Previously we reported that the medial posterior division of the bed nucleus of the stria terminalis (BSTMP) was sexually dimorphic in Wistar and Long–Evans strains while the medial anterior division (BSTMA) and the locus coeruleus (LC) only showed sex differences in the ancestor Wistar strain. The lateral posterior division (BSTLP) was isomorphic in both strains. The present work studies the number of neurons in the BSTMP, BSTMA, BSTLP and LC of male and female Wistar and Long–Evans rats (F 0) and their hybrid F 1 and F 2 generations. The BSTMP is sexually dimorphic in the F 0, F 1 and F 2 generations while sex differences in the LC are only seen in F 0 Wistar rats but not in the F 0 Long–Evans or the F 1 and F 2 hybrid generations. Sex differences in the BSTMA are seen in F 0 Wistar but not in F 0 Long–Evans rats and completely disappear in the F 2 generations. The number of neurons in the LC of both males and females decreased in heterozygotic individuals (F 1) but increased in homozygotic (F 2). However, the number of neurons in the BSTMP changes significantly over the generations, although the ratio of neurons (female/male) is stable and unaffected in homo- or heterozygosis. Thus, the mechanism that regulates the neuronal female/male ratio would be different from the one that controls the number of neurons. The facts that sex differences in the BSTMP are not affected by homo- or heterozygosis and that they are seen in several mammalian orders suggest the existence of a “fixed” type of brain sex differences in the Mammalia Class.