When I was a kid, for my regular check-ups, they always started with me in my tightie-whities. As soon as I got into the exam room I was told to undress to my underwear while my mom sat in the chair.
Once in my underwear, the nurse took vitals - and height & weight (there was a scale in the exam room). I remember that, at least when I was younger, she'd put a glass thermometer in my armpit.
When the doctor came in, at first he'd do the entire exam with me in my underwear. For genital exams, he'd have me laying on the table and just slide his hand under my waistband and manipulate my little erection and my testicles.
At about age 11 all of that changed, and I was told to get completely undressed at the very beginning of the exam, so I was naked for everything, from height & weight to the very end. I remember that they wouldn't tell me to get dressed until after the doctor had finished talking to my mom.
I was 12 when the doctor had me get dressed and go to the waiting room with the nurse while he kept my mom in the exam room to "discuss my development."
After that I started seeing him every 3 months, and then monthly as part of a "boys developmental study" and every exam was naked start-to-finish. That lasted several years, until I entered puberty (rather late).