Children's Health Equity Act of 1999 - Amends title XIX (Medicaid) of the Social Security Act to provide for an increased Federal medical assistance percentage for expanded coverage of certain waivered low-income children in States which: (1) have established a Medicaid applicable income level for children under age 19 that is at or above 200 percent of the poverty line; and (2) demonstrate a commitment to reach and enroll such children. Defines "waivered low-income children" as those whose family income: (1) exceeds certain minimum Medicaid-eligible levels required to be established for the age of the child; but (2) does not exceed the Medicaid applicable income level for that child.

Provides for expansion of the individuals and entities which may serve as qualified entities with regard to the Medicaid presumptive eligibility option for low-income children.

Limits the number of waivered low-income children for a State for FY 1998 and each succeeding fiscal year.