Biodefense and Pandemic Vaccine and Drug Development Act of 2006

Biodefense and Pandemic Vaccine and Drug Development Act of 2006 - Amends the Public Health Service Act to require the Secretary of Health and Human Services to develop and make public a strategic plan to integrate biodefense and emerging infectious disease requirements with the advanced research and development, strategic initiatives for innovation, and the procurement of qualified countermeasures and qualified pandemic or epidemic products.

Establishes the Biomedical Advanced Research and Development Authority (BARDA) within the Department of Health and Human Services (HHS).

Requires the Secretary to: (1) coordinate and oversee the acceleration of countermeasure and product advanced research and development; and (2) delegate to the Director of BARDA any necessary functions and authorities.

Establishes the Biodefense Medical Countermeasure Development Fund.

Requires the Secretary to establish the National Biodefense Science Board to provide expert advice and guidance to the Secretary on matters relating to current and future chemical, biological, nuclear, and radiological agents.

Amends the Federal Food, Drug, and Cosmetic Act to extend the period of market exclusivity from seven years to ten years for certain new drugs, antibiotics, or anti-infective drugs to treat a rare disease or condition caused by a biological agent, toxin, chemical, radiological, or nuclear agent that is deemed by the Secretary to be a material threat to the United States.

Provides an antitrust exemption for: (1) meetings and consultations held by the Secretary among persons engaged in the development of countermeasures or pandemic or epidemic products; and (2) agreements resulting from such meetings.

Prohibits payment on a security countermeasure procurement contract until the delivery of an acceptable portion of such product to the Secretary unless advance payment is necessary to ensure the success of the project.