Gray Market Drug Reform and Transparency Act of 2012 - Amends the Federal Food, Drug, and Cosmetic Act to: (1) make it a prohibited act and a misbranding for a wholesale distributor of prescription drugs to purchase or receive a prescription drug from a pharmacy or a pharmacist, (2) require annual reporting by wholesale distributors of prescription drugs, (3) require the Secretary of Health and Human Services (HHS) to establish and maintain a national database of information reported by wholesale distributors of prescription drugs and to require such database to include information on actions taken by states against wholesale distributors (e.g., disciplinary actions and license revocations), (4) require the Secretary to assess and collect fees from wholesale distributors of prescription drugs, and (5) require wholesale distributors of prescription drugs to provide to recipients of a prescription drug in shortage the sales price for such drug at the time of its sale and at the time of any prior sale of such drug when it was in shortage.