It's from the old-school theories of "medicine" which tells you that illness is due a result of evil spirits in your body. Drilling a hole in your head is the obvious solution to
that problem.
This rates right up there with homeopathy and astrology on my bullshit-o-meter, with the added extra point that trepantation is positively dangerous, in unskilled hands it can cause brain damage (well duh! you
are drilling into someones head) and can leave a wound open to infection.
Interesting and non-judgemental article on Salon:
http://www.salon.com/health/feature/...ion/print.html