Medical regulations list the following 15 medical conditions as specifically disqualifying. If you report having any of them on your medical application, your AME cannot issue a medical certificate until it is cleared by the FAA under what's known as a special issuance authorization.
A special issuance is a two-sided coin. It's great that the regulations offer a mechanism to offset the disqualifying conditions. The downside is that it's a discretionary issuance granted by the Federal Air Surgeon and comes with requirements for periodic interim medical reports and time limitations (usually 12 months) on the duration of the certificate, and it can be withdrawn anytime the FAA sees evidence of an "adverse" change in your condition.
You may hold a certificate that appears to be valid for up to 60 calendar months in accordance with FAR 61.23. In reality, though, the certificate is valid for only as long as the authorization is in force, and that's determined by the type of medical condition and the perceived risk of incapacitation that could result from the condition.
In addition to the time limitation, reissuance of the certificate will be based on additional testing that must be submitted to the FAA prior to the expiration date of the authorization. This might be a simple status report from your treating physician or a complete reexamination with comprehensive (and expensive) diagnostic testing. Additional limitations may be placed on the operational privileges of the certificate, such as limiting a second class medical holder to carrying passengers for hire only when part of a qualified two-pilot crew.
A special issuance is different from a waiver or Statement of Demonstrated Ability (SODA). Waivers are issued for static defects that are not likely to change. Useful vision in only one eye (monocular vision) is one condition for which a medical flight test might be used. There are several hundred pilots flying with monocular vision waivers. Upper or lower limb amputees can also qualify for a SODA with a flight test. Medical flight tests are sometimes conducted to demonstrate that an applicant can safely operate the aircraft.
The waiver becomes part of your medical certificate and shows that, although you don't necessarily meet the minimum standards to hold a medical certificate, you have satisfied the FAA that you can safely exercise the privileges of the certificate(s) you hold.
For special issuance consideration, the FAA will ask for medical information specific to the type of condition you had. Often, that first round of records will be sufficient for the FAA to make a decision. Sometimes, though, additional information is needed, especially if the first records you sent are incomplete or inconclusive, or if there are abnormal results indicated. You may get several letters over a period of months asking for more information before finally getting a decision. That's another reason why TurboMedical® is a valuable tool. You will know exactly what information the FAA requires before you start the process. The doctors in Oklahoma City don't want to ask you for any more information than is necessary, but they also won't issue a certificate until they have a complete medical profile on you. Just be patient and expect a few bumps in the road along the way. The process can be frustrating and time consuming. The hassles notwithstanding, more than 30,000 pilots have been certified under special issuance.
Updated February 2015
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