I live in the U.S. now but I'm originally from Brazil. While in the U.S. males usually stand for the genital exam, most doctors in Brazil will examine your genitals while you're lying down.
The doctor will tell you to strip to your underwear (never a gown!), check height, weight, ask you to lie down, palpate your belly, then tell you to lower your underwear. There is no coughing and another interesting difference: doctors do NOT wear gloves to check your penis and testicles. They only wear gloves for a rectal exam. For the genital portion, they touch you with their bare hands then wash their hands right away. That makes the experience a bit more erotic, I think.
I only had one standing genital exam for a job physical. The doctor told me to take my shirt off then did the whole exam like that. For the genital, he told me to drop my pants and underwear to my knees and only did a visual check. He also turned on a spotlight directed at my crotch area, which made me feel I was putting up a show!