The incidence of mixed chimerism (MC) following allogeneic bone marrow transplantation (allo-BMT) is in part a measure of the marrow ablative effect of preparative regimens. Although the incidence of MC has been reported for many patients treated with total body irradiation (TBI), limited data for busulfan/cyclophosphamide (BU/CY) recipients have been examined. We performed restriction fragment length polymorphism (RFLP) analysis on 68 peripheral blood samples from 26 patients treated with BU/CY prior to allo-BMT for chronic myelogenous leukemia or acute myeloid leukemia. MC was detected in four of 26 patients for an overall incidence of 15.4%. Three of four MC patients are alive with no evidence of disease at 263 to 795 days post-transplantation. A fourth patient is alive at day 501 but developed CNS relapse at day 274. The level of recipient origin cells was less than 10% in all samples and detectable MC was transitory with an RFLP pattern that reverted to full chimerism. These results are comparable to those reported for TBI-containing regimens in patients receiving non-T cell-depleted bone marrow. The efficacy of BU/CY in conjunction with a T cell depletion still requires exploration.