Great Ape Protection Act of 2009 - Prohibits: (1) conducting invasive research on great apes; (2) knowingly breeding, possessing, renting, loaning, donating, purchasing, selling, housing, maintaining, leasing, borrowing, transporting, moving, delivering, or receiving a great ape for the purpose of conducting such research; or (3) using federal funds to conduct such research.
Defines "invasive research" as research that may cause death, bodily injury, pain, distress, fear, injury, or trauma to great apes, including drug testing or exposure to a substance that may be detrimental to the ape's health or psychological well-being.
Requires the Secretary of Health and Human Services (HHS) and other appropriate federal authorities to provide for the permanent retirement of all great apes that are owned or under the control of the federal government and that are being maintained in any facility for the purpose of breeding for, holding for, or conducting invasive research.
Sets forth civil penalties for violations of this Act.