Deadly Biological Agent Control Act of 2001 - Revises Federal criminal code provisions regarding biological weapons to set penalties for: (1) knowingly possessing a select biological agent or toxin (select agent) without obtaining a certification from the Department of Health and Human Services (HHS) under the Antiterrorism and Effective Death Penalty Act of 1996 (AEDPA); and (2) any research facility knowingly transferring a select agent to an entity that has not obtained such certification.

Amends the AEDPA to direct the Secretary of HHS to: (1) annually review the existing list of select agents and, if necessary, revise the list; (2) prioritize countermeasures, including vaccines, therapies, medical devices, and diagnostic tests which must be developed, produced, or obtained in preparation for a bioterrorist attack or other significant disease emergency to treat, prevent, or identify infection by, or exposure to, listed biological agents and toxins (listed agents); and (3) provide for the establishment and enforcement of standards and procedures governing the possession and use of listed agents.

Requires the Secretary to establish a certification process for the possession and use of listed agents. Sets forth legitimate purposes. Requires any individual who handles listed agents to pass a criminal background check, including a determination of whether that individual is a restricted person, and to be registered with the Department of HHS for the specific research project that requires the use of biological agents or toxins.

Sets penalties for violations.