We have used gene marking to investigate the mechanism of relapse and biology of reconstitution following bone marrow transplantation (BMT). The rationale for our initial protocols was to learn if residual malignant cells in autologous marrow contribute to subsequent relapse. Marked malignant cells were found at the time of relapse in 6/8 patients relapsing after autologous BMT for AML or neuroblastoma showing the infused marrow contributed to disease recurrence. Modifications of this marker approach with two distinguishable vectors are now being used to compare the efficacy of purging techniques. We were also able to evaluate gene transfer to normal progenitors and demonstrated that the marker gene was expressed for up to 36 months. Gene marking is also being used to trace the fate of EBV-specific CTLs that we are administering to recipients of allogeneic BMT and has provided evidence of persistence of adoptively transferred CTL for up to 10 months.