Here's one I'm sure very few know: In 855 AD, the Roman Catholic church supposedly unknowingly elected a female pope, who was impersonating a man. When she went into labor in 858, it became impossible to hide that she was a female, and the church responded by executing her.
For a few centuries thereafter, part of the coronation ceremony for new popes was to sit on a chair with a hole in the bottom, with his junk hanging through the hole. A bishop would then have the job of giving the new pope a reach-around, to verify he indeed had testicles, confirmed by the utterance of an official phrase, "Duos habet et bene pendentes". Translated to English, "He has two and they dangle nicely".
There is debate and myth surrounding the chair, which is actually much, much older than the reach-around ceremony, with most evidence pointing toward it being an old and ornate toilet chair that was repurposed for this ceremony.
The Roman Catholic church of course denies all of this today, but like with some other things they've more recently tried to deny, there is too much evidence to completely make the story go away.