I believe this mostly depends on the individual doctor or practice. Until fairly recently I always thought of the phrases physical exam, check-up, annual or yearly, as meaning basically the same thing. My previous PCP, female family med doctor, put me on BP meds when I first started seeing her years ago for a back problem. She told me then that I needed to come in every year or so to make sure there were no problems. When my prescription would run out I would call the office and say I needed a check-up to refill my meds. When the assistant took me back to the exam room, she would always take my BP, temp, etc. and confirm why I was there. She always used the phrase, "You're here for a check-up?". When the doctor saw me we had at most a 5 minute conversation and she examined me for maybe 2 minutes. Looked briefly at my head (sometimes throat, sometimes ears, eyes, nose, it varied every visit) then would listen to my heart and lungs. Sometimes she would do a very brief abdominal exam or thump on my back a bit, sometimes she didn't. I never had to undress at all. Sometimes I had my labs done before the visit and we would go over that, sometimes it was done after and they would call with the results.
This continued for years. Finally as I got older, I started thinking that I wanted a bit more from my healthcare provider. When I called the office the next time, I used the phrase yearly check-up to schedule my next appointment. The assistant this time used the exact same phrase to confirm why I was there, "yearly check-up". I got the exact same exam from the doctor. The next time I called and used the phrase "my annual" to schedule. The assistant once again asked, "You're here for your annual?". I got the same exact exam from the doctor.
Finally, I called to schedule and used the words physical exam. In the exam room the assistant asked if I was there for a physical, and I confirmed that I was. I thought, finally I'm going to get some action! The assistant leaves the room and again I don't have to undress any. No big deal I thought, this can still go in any number of ways when the doctor comes in. Once she came in and sat down, she again confirmed that i am there for a physical. She then had a short conversation, more with herself than me I think, about how that may actually be cheaper and insurance and on and on. She then said with a physical the main difference is we need to make sure I'm doing testicular self exams at home, and that when I turn 50 we discuss prostate exams and if/ when I need to do that. She then conducted the same exact 2 minute exam I'd had for years. I was out the door 5 minutes after she came in. From a medical perspective, if she didn't see a need to examine anything else, then I'm fine with that. From a medfet perspective... what a let down!!!