I've quoted it (slightly edited) because it's typical of the questions I get asked, and the answers I give, in comments in many places. It's useful for me to have the URLs of the scientific articles handy.
I'm curious---how is a "male" brain different from a "female" brain, and how can doctors tell this? (Especially since brains are not easily examined from outside?)
Easy, you cut people up during Autopsies.
Zhou J.-N, Hofman M.A, Gooren L.J, Swaab D.F (1997)
A Sex Difference in the Human Brain and its Relation to Transsexuality. (PDF)
Kruijver F.P.M, Zhou J.-N, Pool C.W., Swaab D.F. (2000)
Male-to-Female Transsexuals Have Female Neuron Numbers in a Limbic Nucleus (PDF)
I mean we have it pounded into us, over and over, that there are no real differences between males and females.
Well, who are you going to believe, Post Modernist Gender Studies Professors who know nothing of biology, or Dynamic MRI Images?
Hamann S, Herman R.A, Nolan C.L, & Wallen K. (2004)
Men and women differ in amygdala response to visual sexual stimuli (PDF)
Of course say that in public, and even presidents of Harvard can get fired for political incorrectness.
As I understand it, sex is determined very early on during gestation, by one's DNA. DNA don't lie.
And thus there are no children born with cleft palates, nor heart defects, the Thalidomide kids did not exist because the DNA don't lie... The DNA is a plan, like an architect's drawing or a blueprint. But things can go awry during construction. Thalidomide caused terrible defects in development of limbs. DiEthylStilbestrol (DES) caused 1 in 5 male children to have feminine brains. But kids are born with such problems randomly anyway.
From the Benjamin's Syndrome Info site (see TS Stuff link list to left):The embryo's DNA is essentially the blueprint from which it knows how to develop. This blueprint contains much more information than the embryo will actually use. Genetic abnormalities can cause errors in the parts of the blueprint that the embryo is using, or tell it to use the wrong parts of the blueprint. So some parts of the body might not know they're supposed to make certain changes when they're exposed to testosterone, for example. Also, the presence of various hormones at various stages during the embryo's development helps regulate which parts of the blueprint are followed. If the wrong hormones are introduced at critical times (eg by the mother taking pills), or something prevents the right hormones from being present, the embryo will not develop as expected.
Abnormalities in sexual differentiation as a group are known as Intersexuality. Androgen Insensitivity Syndrome (AIS) is a good example. Embryos with Total AIS do not recognise testosterone, so their external genitalia is female. However, they are affected normally by AMH, so if they have XY chromosomes they will not develop female internal organs (eg the uterus).
Benjamin's Syndrome is a form of intersexuality in which the brain of a person with XY chromosomes fails to masculinise for some reason, or the brain of a person with XX chromosomes does masculinise (there may be many ways in which this can happen). It is often (but by no means always) accompanied by other signs of mild atypical sexual differentiation, eg a particularly large clitoris or small penis, unusually pronounced proto-labial seam, late or minimal puberty, etc. It can also coexist with other types of intersexuality, though if another kind of intersexuality is present then an additional diagnosis of Benjamin's Syndrome would generally be considered superfluous.