I'm not a biologist by any stretch of the imagination, but I am familiar with some research regarding gender identity and biological causes.  There has been a long term study in the Netherlands that have demonstrated changes in the Bed Stria Terminalus (BST) in the hypothalamus in the brain - it's larger in males than females and in male-to-female transsexuals, the BST is closer is size and shape to a genetic female's BST.  Due to the small sample group, it hasn't yet been determined if this difference is due to genetic reasons or may be caused by other sources, such as hormone therapies.

Dr. Eric Vilain, a urologist at UCLA, who has done a lot of genetic research in gender identity issues has reported in 2003 that there are 54 different genes in the sex chromosomes that may have an influence on gender identity.

Dr. Joan Roughgarden, a biologist at Stanford, authored a book, "Evolution's Rainbow: Diversity, Gender, Sexuality in Nature and People", which makes a case for how homosexuality and transgender identities can have an effect on natural selection. 

As a note for the person stating that "homo" is Greek for man and the root for homosexuality.  "Homo" in Latin means "the same" - this is the root word for homosexuality.