Border Health Security Act of 2006

Border Health Security Act of 2006 - Requires the Secretary of Health and Human Services (the Secretary), acting through the U.S. members of the United States-Mexico Border Health Commission, to award grants to improve border residents' health.

Requires the Secretary to award grants to states, local or tribal governments, or public health entities for bioterrorism preparedness in the border area.

Authorizes appropriations to carry out the United States-Mexico Border Health Commission Act.

Allows the Secretary to coordinate with the Secretary of Homeland Security in establishing a health alert system that: (1) alerts clinicians and public health officials of emerging disease clusters and syndromes along the border area; and (2) is alerted to signs of health threats or bioterrorism along the border area.

Requires the Secretary to enter into a contract with the Institute of Medicine for the study of binational public health infrastructure and health insurance efforts.

Authorizes any member or staff of the Commission to provide advice or recommendations to Congress concerning issues that are considered by the Commission.