A gastroenterologist will want to perform a rectal exam, which will include feeling inside your anus and into your rectum. This is not your vagina so should make no difference whether you have your period or not. This comes from a different place.
Did you mean a proctologist? If so it will not make a difference if you have your period or not. Just let them know that you have it and the nurse will lay down a protective pad called a chux so that the exam table stays clean.