For my LO it was:
Eyes and eyesight (tracking a moving object), ears, mouth, anus, hips, umbilicus, skin, looked at the bottom of his spine, checked his neck strength, weight and length. They also got him to smile but I don't think that was a necessary part of the check.
They asked me about how he has changed and developed from a newborn, how feeding and sleeping was going and if I had any concerns.
He also had his first immunisations but we do them earlier in NZ than you do over there.