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Yes there is. Women that are at least partially transitioning to male are called Transgender men and males that are at least transitioning to female are called Transgender women. There is also a biological difference between transgendered individuals and non-transgendered individuals.

A transgender person is someone who is at odds with the gender role assigned to them by society. Or they are one whose internal representation of their gender differs from the classic polar binary theory of gender. Each person in this group is different from each other, so there certainly is a difference between male and female but there are few areas that everyone shares.

In terms of transsexuals rather than transgenders, a transsexual person wishes to have their physical/outward sex changed to match what is inside. In this, the difference in males and females is the physical surgery (if any) used and the hormones used in HRT.

The surgical procedure for FTM (female-to-male) is a lot different than the one for MTF (male-to-female) transgender individuals. There has been anecdotal evidence that the brains of transsexuals are different from that of the assigned sex and often more like the sex they wish to physically be. No brain studies have likely been done on transgender persons who are not interested in surgery and complete transition.

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