Safeguarding America's Pharmaceuticals Act of 2011

Safeguarding America's Pharmaceuticals Act of 2011 - Amends the Federal Food, Drug, and Cosmetic Act to require the Secretary of the Treasury to destroy imported counterfeit drugs and adulterated or misbranded imported drugs with a value of less than $2,000.

Requires the manufacturer of a prescription drug to provide to its wholesale distributors or dispensers a packing list or comparable document containing identifying information, including the National Drug Code number, container size, and lot number of the drug.

Requires each manufacturer or repackager of a prescription drug to: (1) apply a standardized numerical identifier that is unique to each unit of the drug to at least 50% of its drugs by January 1, 2015, and to all of its drugs by January 1, 2016; and (2) notify the Secretary of Health and Human Services (HHS) of the method it will use to meet such requirement.

Requires the Secretary to establish an effective drug identification and tracking system to authenticate the wholesale distribution history of any prescription drug that is subject to a requirement for a standardized numerical identifier.

Expands the requirements for the licensing of wholesale distributors, including to require mandatory background checks. Disqualifies a person who has been convicted of certain felonies or who has engaged in a pattern of violative behavior.

Establishes civil monetary penalties for violations of this Act. Requires penalties paid to the United States to be used by the Secretary of HHS to prevent and address unlawful counterfeiting and diversion of drugs.

Authorizes a state to enforce the requirements of this Act under certain circumstances.

Requires the Secretary of HHS to study threats to the domestic prescription drug supply chain.