I do not know if this has changed during the recent decades, but indeed in the past it was standard in all countries for the military fitness physical exam to be done nude (for males).

Moreover, it was completely pointless to be shy about this, because if you were conscripted, the norm was to have common showers, so anyone could have a good look at you for much more than the few seconds of the physical exam.

Then why girls don't have to show their genitals during medical exam?

EDIT. I'm serious. Few girls are summoned (e.g. medical related education). They don't have to show their genitals.