Previous work has demonstrated that the GABAergic system is involved in sexual differentiation of the rodent hypothalamus. The present study was designed to further examine this involvement by investigating developmental sex differences in GAD 65 protein levels in hypothalamic and extrahypothalamic brain regions known to be sexually dimorphic in adulthood. Brain nuclei were micro-dissected and GAD 65 protein levels were quantified using western immunoblotting. Sex differences in levels of GAD 65 were found in the dorsomedial nucleus and preoptic area of the hypothalamus and also the medial amygdaloid nucleus and CA1 subfield of the hippocampus. Unexpectedly, there were sex differences in protein levels of the housekeeping gene, GAPDH, cautioning against the use of GAPDH for standardizing protein samples during western immunoblotting.