Native American Housing Enhancement Act of 2003

Native American Housing Enhancement Act of 2003 - Amends the Native American Housing Assistance and Self-Determination Act of 1996 to define, with respect to a dwelling unit, "fair market rent" as one, determined at least annually by the Secretary of the Interior, for existing or newly constructed dwelling units of a size and type similar to, and located in the same market area as, the dwelling unit.

Modifies program requirements concerning rents and housing payments. Provides that, in the case of a low-income family residing in a rental dwelling unit assisted with grant amounts under this Act, the monthly rent for the dwelling unit shall not exceed the fair market rent. States that, if such a family resides in a lease purchase dwelling unit assisted with such grant amounts, the monthly homebuyer payment shall not exceed, at the recipient's election, either 30 percent of the monthly adjusted family income, or the fair market rent.

Prohibits the Secretary from requiring mandatory recertification of the incomes of families residing in rental or lease purchase dwelling units assisted with such grant amounts.

Requires grant recipients to reserve amounts out of such grants to ensure payment of: (1) principal and interest as it becomes due on any bonds or other obligations relating to the housing; and (2) the costs of insurance and administrative expenses for such housing.

Prohibits the Secretary from restricting access to, as well as reducing, a grant amount for any Indian tribe based solely on certain conditions relating to retention of grant income.

Amends the Housing Act of 1949 to declare that the giving of a preference to members of an Indian tribe for the use of any dwelling or other building constructed, improved, altered, repaired, replaced, or otherwise aided with assistance provided under such Act to the Indian tribe shall not constitute a violation of the Civil Rights Act of 1964.

Amends the Cranston-Gonzales National Affordable Housing Act to make Indian tribes, tribally designated housing entities, or other agencies primarily serving Indians eligible for Youthbuild grants.