Medicare Prescription Drug Program Integrity and Transparency Act of 2013

Medicare Prescription Drug Program Integrity and Transparency Act of 2013 - Amends part D (Voluntary Prescription Drug Benefit Program) of title XVIII (Medicare) of the Social Security Act to require each contract entered into with a prescription drug plan (PDP) sponsor with respect to a PDP the sponsor offers to prohibit the PDP from entering into a contract with any pharmacy benefits manager (PBM) to manage the prescription drug coverage provided under such plan, or to control the costs of the prescription drug coverage under it, unless the manager satisfies specified PBM audit and disclosure requirements.

Requires a PBM to provide: (1) a particular aggregate average reimbursement rate for generics or a maximum average discount off of an accepted pharmaceutical pricing benchmark for multi-source generics as a whole ("generic effective rate"), and (2) a process for the generic effective rate to be appealed.

Revises requirements for contracts with PDP sponsors to require that the PDP sponsor or a subcontractor of the sponsor disclose to a pharmacy, at the time when a contract is offered and at least once every seven days, the methodology and actual per unit reimbursement amount for each covered drug for each contracted pharmacy.