If the commander decides to take a chance and ask for a waiver, where it goes from that point depends on the branch of the service you're joining (see the bottom of the medical standards page ). However, in a nut-shell, it winds its way across the desks of several military medical officials, each one reviewing it and recommending approval or disapproval, until it finally falls into the hands of a high-ranking doctor with birds or stars on his/her shoulders who makes the ultimate decision.
If the Medical Waiver God disapproves the waiver, then that's the end of the road for any chance you have of joining that branch of service. There are no appeals to medical waiver disapproval (the waiver process *is* the appeal).
Contacting Your Congress Person
If your medical waiver is disapproved, your recruiter may tell you that your only appeal is to contact your Congressman. This is what some recruiters tell applicants, basically just to get the applicant off their backs. I have never once, not even a single time seen, or even heard of a congressional inquiry overturning a medical waiver denial. Under the law, and DOD regulations, the individual service has the absolute right to decide whether or approve or disapprove medical waivers, depending on the current "needs of the service." A Congressional inquiry won't change anything, in my honest opinion (and experience).
Waiver approval/disapproval is only applicable for that particular branch of service. If your waiver is disapproved by the Navy, for example, you can walk across the hall to the Army recruiting office, and it's possible that the Army would give favorable consideration for a waiver. Conversely, if the Navy approves a medical waiver, you could not use that waiver to join the Army.
I'm often asked questions such as "My waiver for xyz condition was disapproved, but I know of people on active duty that have the same condition. How come my waiver was disapproved?"
Apples and oranges. As an applicant, the Military has very little time and money invested in you. They have lots of time and money already invested in that active duty member, however. If a medical condition is diagnosed after one is on active duty (assuming it's not a pre-existing condition that the member lied about, which is an entirely different story), the Military isn't going to discharge them unless a Medical Evaluation Board determines the member can't perform his/her duties.