Public Research in the Public Interest Act of 2006 - Requires, as a condition of receiving federal assistance, any institution of higher education or research that conceives, reduces to practice, or holds title in a subject invention to grant irrevocable, perpetual, nonexclusive licenses to the invention and associated rights to any party requesting such a license pursuant to this Act. Provides that licenses shall be issued for: (1) supplying medical products to countries with low-income or lower-middle income economies; or (2) conducting neglected research anywhere, royalty-free. Provides that such licenses shall be part of the institution's title in a subject invention. Makes a license under this Act irrevocable and perpetual so long as the licensee submits to the licensor payment of a fair royalty on sales of any medical product within 90 days.

Deems a party as automatically receiving the license requested upon submitting the required information to the Food and Drug Administration (FDA). Sets forth procedures for objections to the grant of a requested license.

Requires the holder of title or any license in a subject invention to notify the FDA of any grant or license of rights in that invention.