Health Care for the Homeless Act of 1988 - Amends the Public Health Service Act to increase the portion of a grant for the delivery of health services to homeless individuals which must be provided by the grant recipient from non-Federal funds for fiscal years after the first fiscal year from 25 percent to 33 1/3 percent. Permits the Secretary of Health and Human Services to waive such requirement if the applicant is a nonprofit private entity and other conditions are met. (Current law permits the Secretary to waive the requirement if the applicant is a nonprofit private grantee under provisions of the Act relating to community health centers and if the same conditions are met.)

Permits grant recipients who have provided health or mental health services to a homeless individual to continue to provide the services from grant funds for 12 months after the individual becomes a resident in permanent housing.

Amends the definition of "homeless individual" to include an individual who is in transitional housing.

Amends provisions permitting the Secretary to provide grantees technical assistance to make the limit on expenditures for the assistance apply to a fiscal year. (Current law sets the limit but does not state whether the limit is applicable per fiscal year.)

Authorizes appropriations for FY 1989 through 1991.