Hospital Indigent Care Assistance Act of 1989 - Title I: Amendments of Internal Revenue Code of 1986 - Amends the Internal Revenue Code to impose on employers an excise tax equal to one percent of the amounts paid by an employer to provide employee medical benefits.

Subjects self-employed individuals to a corresponding tax based on the amount allowed as a tax deduction for health insurance costs.

Establishes in the Treasury the Hospital Indigent Care Assistance Trust Fund to receive amounts generated by the excise tax. Makes Fund moneys available solely for Medicare program expenditures.

Title II: Assistance to Hospitals Providing Indigent Care - Amends title XVIII (Medicare) of the Social Security Act to direct the Secretary of Health and Human Services to make payments from the Fund to eligible applicant hospitals to cover a specified percentage of their uncompensated care costs, determined in accordance with this Act. Describes eligibility criteria, including a requirement that the Medicare allowable costs of providing patient care services exceed the hospital's patient revenues for the pertinent cost reporting period.

Directs the Secretary to: (1) provide for a study of the extent of uncompensated health care provided by various health care providers; and (2) report the results to the Congress by July 1, 1992.