Afghan Women Empowerment Act of 2006 - Expresses the sense of Congress that the protection of the rights of women and girls in Afghanistan and their full participation in the reestablishment of democracy are essential to Afghanistan's reconstruction, and to achieve such reconstruction the U.S. government must commit resources to advance the rights of women throughout Afghanistan.
Amends the Afghan Freedom Support Act of 2002 to revise the provisions respecting assistance to women and girls in Afghanistan. Extends funding authority. Expresses the sense of Congress that the President should: (1) condition the provision of such assistance on the recipient adhering to international standards for women's rights and human rights; and (2) ensure that Afghan women-led nongovernmental organizations with demonstrated experience in delivering services to Afghan women and children receive grants without ethnic, religious, or any other discrimination.