The primary FARs concerning medical certification are in 14CFR67
Here is a list of explicitly disqualifying conditions, which may with proper documentation, still allow medical certification with a Special Issuance. When applying for a Special Issuance the first time, the AME must defer a decision to AMCD Aerospace Medical Certification Division of the FAA in Oklahoma City or even to FAA Headquarters in Washington, but if the condition(s) are stable, many conditions are now considered AASI. In other words, the AME can issue a medical during renewals.
There is no official, public regulation about medical drugs which are acceptible or not for medical certification. Some general rules include that the FAA waits a year after FDA approval so as to collect some post-marketing surveillance data. Recently, the FAA released a No Issue / No Fly list of drug categories. If you are taking and medications, please review this list with your personal doctor before your AME appointment. There is another unofficial drug list from AOPA that may be helpful also.
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