Sex steroid hormones act on developing neural circuits regulating the hypothalamic-pituitary-gonadal axis and are involved in hormone-sensitive behaviours. These hormones act mainly via nuclear receptors, such as oestrogen receptor (ER)-α and androgen receptor (AR). By using immunohistochemistry, we analysed the expression level of ERα and AR throughout perinatal life [at embryonic (E) day 19 and postnatal (P) days 5, 15 and 25] and in adulthood in several hypothalamic nuclei controlling reproduction in both wild-type and aromatase knockout (ArKO) (i.e. which cannot convert testosterone into oestradiol) mice to determine whether there are sex differences in hypothalamic ERα and AR expression and, if so, whether these are established by the action of oestradiol. As early as E19, ERα immunoreactivity (-IR) was observed at same expression levels in both sexes in the anteroventral periventricular nucleus (AVPv), the medial preoptic area (MPOA), the bed nucleus of the stria terminalis (BnST), the ventrolateral part of the ventromedial hypothalamic nucleus and the arcuate nucleus (ARC). Sex differences (female > male) in ERα-IR were observed not only during the prepubertal period in the BnST (P5 to P25) and the MPOA (P15), but also in adulthood in these two brain regions. Sex differences in AR-IR (male > female) were observed at P5 in the AVPv and ARC, and at P25 in the MPOA and ARC, as well as in adulthood in all hypothalamic regions analysed. In adulthood, gonadectomy and hormonal treatment (oestradiol or dihydrotestosterone) also strongly modulated ERα-IR and AR, respectively. Taken together, sex differences in ERα-IR and AR-IR were observed in all hypothalamic regions analysed, although they most likely do not reflect the action of oestradiol because ArKO mice of both sexes showed expression levels very similar to wild-type mice throughout perinatal development.