Vaccines for the New Millennium Act of 2005

Vaccines for the New Millennium Act of 2005 - Directs the President to establish a strategy to accelerate efforts to develop vaccines and microbicides for neglected diseases such as HIV/AIDS, malaria, and tuberculosis, which shall: (1) expand public-private partnerships; (2) create economic incentives for such vaccines' research, development, and manufacturing; (3) include the negotiation of advanced market commitments; (4) address related intellectual property and regulatory approval issues; (5) maximize U.S. capabilities to support clinical trials in developing countries; (6) expand the purchase and delivery of existing vaccines; and (7) address the challenges of advance delivery of vaccines in developing countries.

Directs the Secretary of the Treasury to: (1) enter into negotiations with the World Bank, the International Development Association, Global Alliance for Vaccines and Immunizations, and other interested parties to establish advanced market commitments to purchase such vaccines and microbicides; and (2) establish in the Treasury the Lifesaving Vaccine Purchase Fund.

Amends the Internal Revenue Code to establish business credits for: (1) vaccine research related to HIV/AIDS, malaria, tuberculosis, or certain infectious diseases afflicting developing countries; and (2) certain sales of lifesaving vaccines to nonprofit organizations, or to foreign governments or instrumentalities for distribution in developing countries.

Amends the Small Business Act to: (1) direct the Small Business Administration (SBA) to establish a four-year pilot program to encourage the development of such vaccines and microbicides, including program outreach activities; and (2) provide Small Business Innovation Research Program (SBIR) and Small Business Technology Transfer Program (STTR) funding for such vaccines and microbicides.