Prenatal programming and biasing work through alterations of the nervous system; thus can be said to reflect brain sex. During prenatal development the nervous system, the brain in particular, is programmed along a track that is usually concomitant with the development of other sex appropriate structures like genitals and reproductive organs. The brain, however, as in other Intersex conditions, can develop along one sex/gender path while other organs develop along another. Put simply, the brain can develop as male while other parts of the body develop as female. Further, it is important to recall that the developing nervous system controlling gender-linked behaviors is more sensitive to certain stimuli than are the tissues forming genitals and thus can be modified while the genitals are not. I think that transsexuals are intersexed in their brains.Exactly.
Then there's this PDF diagram, which supposedly is satirical, though I've not found any area where it wasn't completely correct. It even gives references.