National Mental Health Parity Act of 1999 - Title I: Parity for Treatment of Mental Illness - Amends the Internal Revenue Code to impose on the applicable issuer a tax equal to 25 percent of a health plan's premiums received during the calendar year if the plan imposes additional applications, preadmission screenings, or other procedural restrictions for services, or imposes treatment limitations or financial requirements on the coverage of benefits provided with respect to any of specified psychiatric disorders (described in the American Psychiatric Association's Diagnostic and Statistical Manual), while similar limitations or requirements are not imposed on coverage of benefits with respect to other conditions. Provides similar obligations and sanctions with respect to group health plan parity for treatment of mental illness.

Title II: Medicare Mental Health Improvement - Amends title XVIII (Medicare) of the Social Security Act to restructure the mental health benefit, including: (1) coverage under Medicare part A (Hospital Insurance) of inpatient hospital services furnished primarily for the diagnosis or treatment of mental illness or substance abuse for up to 60 days during a year, as well as coverage of intensive residential services furnished to an individual for up to 120 days during a year; (2) lower co-payments for certain outpatient mental health and substance abuse services; (3) waiver of co-payment for case management services furnished to a seriously mentally ill adult, a seriously emotionally disturbed child, or an adult or child with serious substance abuse disorder; (4) case management services for an unlimited duration for such individuals; and (5) provision of items and services furnished under Medicare part B (Supplementary Medical Insurance) for the treatment of mental illness or emotional disturbances according to standards established by the Secretary of Health and Human Services.