Zhou et al. (1995)
It found that in a region of the brain called the bed nucleus of the stria terminalis (BSTc), a region known for sex and anxiety responses, MTF transsexuals have a female-normal size while FTM transsexuals have a male-normal size. While the transsexuals studied had taken hormones, this was accounted for by including non-transsexual male and female controls who, for a variety of medical reasons, had experienced hormone reversal.
www.nature.com/nature/journal/v378/n6552/abs/378068a0.html
Kruijver et al. (2000)
looked at the number of neurons in BSTc instead of volumes. They found the same results as Zhou et al. (1995), but with even more dramatic differences. One MTF subject who had never gone on hormones was also included, and who matched up with the female neuron counts nonetheless.
press.endocrine.org/doi/abs/10.1210/jcem.85.5.6564
In 2008, a new region with properties similar to that of BSTc in regards to transsexualism was found by Garcia-Falgueras and Swaab: the interstitial nucleus of the anterior hypothalamus (INAH3), part of the hypothalamic uncinate nucleus. The same method of controlling for hormone usage was used as in Zhou et al. (1995) and Kruijver et al. (2000). The differences were even more pronounced than with BSTc; control males averaged 1.9 times the volume and 2.3 times the neurons as control females, yet once again, regardless of hormone exposure, MTF transsexuals lay within the female range and the FTM transsexual within the male range.
brain.oxfordjournals.org/content/131/12/3132
Luders et al. (2009),
24 MTF transsexuals not-yet treated with cross-sex hormones were studied via MRI. There was a significantly larger volume of gray matter in the right putamen compared to men. As with many earlier studies, they concluded that transsexualism is associated with a distinct cerebral pattern. Although it did show that regional gray matter concentrations were more similar to men than women.
www.ncbi.nlm.nih.gov/pmc/articles/PMC2754583/
Rametti et al. (2010)
An additional feature was studied in a group of FTM transsexuals who had not yet received cross-sex hormones: fractional anisotropy values for white matter in the medial and posterior parts of the right superior longitudinal fasciculus (SLF), the forceps minor, and the corticospinal tract. They discovered that, "Compared to control females, FtM showed higher FA values in posterior part of the right SLF, the forceps minor and corticospinal tract. Compared to control males, FtM showed only lower FA values in the corticospinal tract."
www.journalofpsychiatricresearch.com/article/S0022-3956%2810%2900158-5/abstract
Ramachandran (2008)
They found that while nearly two thirds of non-transsexual males who have a penis surgically removed experience the sensation of a phantom penis, only one third of MTF transsexuals do so after sex reassignment surgery. This study, however, overlooks the differences between an amputation, where the nerves connecting the penis and the brain are severed, and male-to-female gender reassignment surgery, where some of the penis and scrotum may be reused to create a vaginal canal, labia and a clitoris. In this case, some of the nerves connecting the new genitalia to the brain remain largely intact. Also, two-thirds of FTM transsexuals reported the sensation of a phantom penis from childhood onwards, complete with phantom erections and other phenomena.
www.ingentaconnect.com/content/imp/jcs/2008/00000015/00000001/art00001?token=003a1640522e8f7e2a46762c6b665d7a663b2553236e457a673f582f47
Berglund et al. (2008),
Tested the response of gynephilic MTF transsexuals to two sex pheromones: the progestin-like 4,16-androstadien-3-one (AND) and the estrogen-like 1,3,5(10),16-tetraen-3-ol (EST). Despite the difference in sexuality, the MTFs' hypothalamic networks activated in response to AND, like the androphilic female control groups. Both groups experienced amygdala activation in response to EST. Male control groups (gynephilic) experienced hypothalamic activation in response to EST. However, the MTF subjects also experienced limited hypothalamic activation to EST as well.
The researchers' conclusion was, that in terms of pheromone activation, MTF's occupy an intermediate position with predominantly female features.
cercor.oxfordjournals.org/content/18/8/1900
Schneider, Pickel, and Stalla (2006)
Prenatal androgen exposure, the lack thereof, or poor sensitivity to prenatal androgens are commonly cited mechanisms to explain the above discoveries. Schneider, Pickel, and Stalla (2006) found a correlation between digit ratio (a generally accepted marker for prenatal androgen exposure) and male to female transsexualism. MTF transsexuals were found to have a higher digit ratio than control males, but one that was comparable to control females.
Hare et al.
The androgen receptor (AR), also known as NR3C4, is activated by the binding of testosterone or dihydrotestosterone, where it plays a critical role in the forming of primary and secondary male sex characteristics. They found that male-to-female transsexuals were found to have longer repetitions of the gene, which reduced its effectiveness at binding testosterone.
www.ncbi.nlm.nih.gov/pmc/articles/PMC3402034/
A variant genotype for a gene called CYP17, which acts on the sex hormones pregnenolone and progesterone, has been found to be linked to female-to-male transsexualism but not MTF transsexualism. Most notably, the FTM subjects not only had the variant genotype more frequently, but had an allele distribution equivalent to male controls, unlike the female controls. The paper concluded that the loss of a female-specific CYP17 T -34C allele distribution pattern is associated with FtM transsexualism.
www.fertstert.org/article/S0015-0282%2807%2901228-9/abstract