It appears that it may be innate and, as Harry Benjamin pointed out, after the age of four that gender identification cannot be altered. The unfortunate case of David Reimer helped us understand this and his forced gender reassignment advocated by John Money did not work because, in spite of being reared as a girl, his internal sense of gender was always male.
This is one way we have come to know that male to female transsexualism is real and why the identification of these children is unwavering and cannot be impacted via psychotherapy. Only the individual's own refusal of self acceptance and intensity of dysphoria will help determine an outcome.
Conversion therapy on strongly dysphoric children doesn’t work and the now retired CAMH practitioner Kenneth Zucker may or may not have had success with children who were borderline. Perhaps some were simply future homosexuals who would come to outgrow their temporary practices. Others who would not demonstrate overtly effeminate traits would not even have been brought to him and simply hid much longer.
So with an early biological component in place we are left to wonder how much socialization can impact this early imprinting. It should be intuitive to state that if the child grows up in a non-accepting environment, the journey should be that much more difficult. It is clear that in the Reimer case, where dysphoria was not present, no amount of socialization could affect his core gender identity.
Afterwards, puberty adds another layer of complexity with two possible roads for these children who will either become woman-loving or man-loving. But even here things are not clear cut since sexual orientation has been known to shift after hormone replacement therapy.
But viewing gender outside of the biological imperative to reproduce should make it easier to accept transsexualism and that its sufferers who transition are women. After all what is the difference between a transitioned woman and a biological one who cannot conceive if neither has ever identified as a male from the outset?
This condition may be an anomaly but it is one that nature created hence detractors cannot blame the patient. This is why I am always astonished at the stupidity of social conservatives who use DNA and chromosomes in their arguments as if somehow this knowledge would cure transsexuals. Regardless, it appears that the condition is independent of genetic architecture and likely originates in a brain which, in every other respect, is in perfect working order.