Allogeneic bone marrow transplantation (BMT) is the only treatment with a potential to cure chronic granulocytic leukemia (CGL). Cytogenetic markers, including the Philadelphia chromosome (Ph), t(9;22)(q34;q11), allow follow-up of these patients after BMT for engraftment and remission status. A variety of cytogenetic patterns have been observed after BMT for CGL. A number of patients experience cytogenetic relapse or mixed chimerism with normal cytogenetics. Furthermore, these types of complications may increase after T-cell depleted BMT. We have closely followed six patients with Ph-positive CGL treated with T-cell depleted bone marrow for 169–720 days after BMT. A number of different cytogenetic patterns were found. The first patient, transplanted while in accelerated phase, relapsed at 155 days with the same clonal abnormalities and died in blast crisis. Four other patients were found to have cytogenetic relapses between days +41 and +233. In every case the Ph reappeared along with other clonal and nonclonal abnormalities, some of which were transient. All four patients presented with hematologic relapse several months after cytogenetic relapse. The final patient has mixed chimerism with Ph-negative cells and continues to be in clinical remission. Close cytogenetic follow-up of CGL patients after BMT can provide important information about early changes in engraftment and remission status.