Vaccines for the New Millennium Act of 2000 - Amends the Foreign Assistance Act of 1961 to restate as the goal for the protection of children from immunizable diseases the universal protection of all children from such diseases by December 31, 2009.

(Sec. 4) Authorizes appropriations for FY 2001 and 2002 for U.S. contributions to: (1) the Global Alliance for Vaccines and Immunizations; and (2) the International AIDS Vaccine Initiative. Requires the President to include in a required report for such fiscal years information on the effectiveness of the above Global Alliance in meeting its immunization and research and development goals.

(Sec. 5) Amends the Internal Revenue Code to provide a business tax credit of 30 percent of qualified vaccine research expenses for a taxable year. Includes as appropriate vaccine research research with respect to malaria, tuberculosis, HIV, or any infectious disease which causes over one million deaths annually. Prohibits such credit from being taken into account when determining the current credit allowed for increasing research expenditures. Prohibits the credit for any research conducted outside the United States. Expresses the sense of Congress that if such credit is allowed, then the corporation receiving such credit should certify to the Secretary of the Treasury that, within one year after that vaccine is licensed, such corporation will develop a good faith plan to maximize international access to high quality and affordable vaccines. Directs the Institute of Medicine to conduct a study of the effectiveness of such credit in stimulating vaccine research, and to report study results to Congress.

(Sec. 6) Provides a lifesaving vaccine sale credit equal to the amount of qualified vaccine sales for a taxable year. Defines a lifesaving vaccine as one which is approved by the Food and Drug Administration and used for malaria, tuberculosis, HIV, or any infectious disease which causes over one million deaths annually. Provides total credit limits for 2002 through 2010 (zero credit after 2011). Provides credit limit allocation and authorized carryover.

(Sec. 7) Establishes in the Treasury the Lifesaving Vaccine Purchase Fund for purchases of eligible vaccines defined earlier under this Act for distribution to developing countries. Limits to $100 million Fund expenditures in a fiscal year. Appropriates funds for the Fund.

(Sec. 8) States that the President should enter into negotiations with officials of foreign governments and other interested parties for the establishment of an international vaccine purchase fund that would: (1) accept contributions from governments of developed countries; (2) use such contributions to purchase and distribute eligible vaccines in developing countries; and (3) be a significant market incentive for private sector vaccine research. Requires an annual report from the President to Congress.

(Sec. 9) Establishes the Lifesaving Vaccine Advisory Commission to: (1) review the progress of national and international efforts to develop eligible vaccines; (2) examine the merits of innovative vaccine research financing that combines public subsidies with private sector research and development efforts; and (3) develop consensus among industry and public health advocates on policy recommendations for ways in which the Federal Government can further advance public-private partnerships in vaccine research and development. Requires a final report from the Commission to the President and Congress.

(Sec. 10) Expresses the sense of Congress that flexible or differential pricing for vaccines which provide lower prices for the poorest countries is one of several valid strategies to accelerate the introduction of vaccines in developing countries.