Intratumoral heterogeneity has been proposed as a possible basis for immunotherapeutic failure when tumor-specific agents such as tumor infiltrating lymphocytes (TIL) are employed for cancer therapy. To examine this issue, highly specific oligoclonal MHC class I-restricted cytolytic TIL grown in bulk culture from patient 397 were used to immunoselect a TIL-resistant variant tumor from the autologous cultured melanoma line 397-mel. Four cycles of immunoselection produced tumor 397-R4, a variant completely resistant to 397 TIL but not to allogeneic LAK cell lysis in 4-h 51Cr release assays. By flow microfluorometry analysis, this tumor variant had not lost MHC molecules, adhesion molecules, or a variety of tumor-associated Ag expressed by the parent tumor but showed decreased expression of many Ag examined. Failure of 397-R4 to cold target inhibit TIL lysis of 397-mel suggested that cell-surface modification was at least one mechanism causing TIL resistance. The inherent lysability of 397-R4 was equal to 397-mel, as confirmed by lectin-dependent cellular cytotoxicity, lysis by non-MHC restricted allogeneic TIL, and lysis by a second line of 397 TIL grown independently from tumor 397. Treatment of 397-R4 with IFN-alpha or IFN-gamma, +/- TNF-alpha for 72 h before cytolytic assays enhanced TIL lysis of this target slightly, and enhanced surface expression of MHC class I and II molecules and the adhesion molecule ICAM-1. The resistant phenotype of 397-R4 was evident in all clones of 397-R4 examined and has been maintained in serial culture for over 13 mo and through passage in nude mice, suggesting that such stable tumor variants may provide an in vivo escape mechanism from specific immune reagents such as TIL. Evolving patterns of TIL culture clonality over time, as well as the spontaneous emergence of different clones in two long term TIL cultures grown under identical conditions from the same source of cryopreserved tumor, were documented by analyzing TCR gene rearrangements and suggest that TIL from different culture passages or lines may be used to overcome resistant tumor subpopulations.