In my research I did hear about the 'sworn virgins' of Albania, and that they might be transgender men. But aside from that, I don't really know about being transgender in the rest of Europe.

The current interest in all things transgender is really fascinating; I wish I knew what it meant!

You state:

Considering at least 0.7% of people today do not identify as their assigned gender, this must have all happened often.

I’m not an expert on the topic by any means but I’m interested in where you got that figure from and I’d be most appreciative if you could point me to the source. The most recent study of the issue I can find is an article entitled, ‘ Epidemiology of Gender Identity Disorder: Recommendations for the Standards of Care of the World Professional Association for Transgender Health’ in the International Journal of Transgenderism 2009. They conclude that GID has not been studied formally by epidemiological methods and thus they rely instead on prevalence estimates derived from indirect methods (clinical presentation, etc.). It could well be that this work is out of date of course and things have moved on, but as of 2009 any population figures for those whose gender identification lies outside of the traditional male/female binary looks to be pretty speculative.

Also, it would be pretty speculative I think to assume that present day prevalence rates, even if accurate epidemiological data existed, can be assumed to mirror historical rates or are universal across different geographical regions. Although one’s views on that topic are likely to be informed by one’s take on the possible causal elements underlying gender identification – social, cultural, biological, etc. Nonetheless, the notion that current ‘western’ conceptions of gender or the transgender are transhistorical is questionable.

In any case, it’s been a while since I looked at any of this and that was only as an undergraduate so my sources may well be out of date, but if I was interested in this topic I’d start with medieval conceptions of gender. Thomas Laqueur’s book, Making Sex (1990) would seem a good place to start. It’s not without its faults (it relies heavily on elite and medical texts and ignores regional differences etc.). It argues that until the early 19th century, there was a one-sex model of the body (derived from Galen) in Europe where the male and female body were seen as different in degree but not kind (that male and female essentially shared the same sexual organs but that women’s organs were inverted into the body) and that with this unitary model there were many genders.

It’s quite possible, however, that Laqueur is incorrect in attributing this belief to the medieval rather than antique and early modern periods. As such, Joan Cadden’s Meanings of Sex Difference in the Middle Ages: Medicine, Science, and Culture (1993), which argues that medieval Christians strongly believed in binary model of gender that reduced the, say, anatomically ambiguous (e.g. hermaphrodites) to conventional categories of masculine and feminine (masculine women, etc), might be a good supplement.

There's also a significant literature on transvestite and transgender saints (mostly FTM) that might be worth checking out (bearded saints, etc; plays on association of virile with spiritual and carnal/physical/the body with the female), but I can't think of any suitable texts off-hand.

It could be (and I hope) that someone else here might have a more up-to-date take on the historical literature on this subject.