But there ' s more to sexgender than just your chromosomes . Chromosomes are just instructions , and instructions can be carried out incorrectly . There ' s also how those genes are expressed . What your body physically looks like and how your brain is wired up . Regardless of your chromosomes everyone starts off female in the womb , the Y chromosome causes the expression of the male genes in the womb and the fetus develops the male physical traits . All manner of development diseases exist where people don ' t express their genes properly in the womb and are born with defects . I don ' t see why it ' s so far fetched that conversion process could mess up in development and cause you to end up with someone with a male brain and a female body , or vice versa , or somewhere in the middle . It makes perfect scientific sense .