Protection Against Transmission of HIV for Women and Youth Act of 2006 - States that it shall be U.S. policy to: (1) pursue a global HIV prevention strategy that emphasizes the needs of married and unmarried women and girls and addresses the factors that lead to gender disparities in HIV infection rates; and (2) balance funding for HIV prevention methods.
Directs the President to: (1) formulate and submit to the appropriate congressional committees, and make available to the public, a comprehensive and culturally appropriate global HIV prevention strategy that addresses the HIV vulnerability of married and unmarried women and girls and seeks to reduce the factors that lead to gender disparities in HIV infection rates; (2) ensure that the United States coordinates its overall HIV/AIDS policy and programs with foreign governments, international organizations, other donor countries, and indigenous organizations; (3) provide clear guidance to U.S. field missions; and (4) implement a monitoring and evaluation system.