Graduate Medical Education Technical Amendments of 1999 - Amends part D (Miscellaneous) of title XVIII (Medicare) of the Social Security Act, as amended by the Balanced Budget Act of 1997 (BBA '97), with respect to the ceiling on the total number of full-time equivalent interns and residences in allopathic and osteopathic medicine in either a hospital or nonhospital setting for purposes of indirect and direct graduate medical education (GME) payments. Repeals the current limitation on program residents in a hospital with respect to the hospital's most recent cost reporting period ending on or before December 31, 1996. Replaces such limitation with one based on the number of residents who were appointed by a hospital's approved medical residency training program for such reporting period. Provides that beginning on or after January 1, 1997, in the case of a hospital that sponsors only one allopathic or osteopathic residency program, the new limit determined above for such hospital may, at the hospital's discretion, be increased by one for each calendar year but shall not exceed a total of three more than such limit.

Limits to programs established between January 1, 1995, and September 30, 1999, (currently, programs established on or after January 1, 1995) the mandate for special rules applying limitations on interns and residents in any kind of medical residence training program. Requires the Secretary of Health and Human Services, in promulgating such rules, to include in the special consideration for facilities meeting the needs of underserved rural areas any facility not located in an underserved rural area which has established a separately accredited rural training track.

Makes this Act's amendments effective as if included in the enactment of BBA '97.