Until recently, cytogenetic detection of the Philadelphia chromosome (Ph) was the only reliable test to diagnose chronic myelogenous leukemia (CML) and detect minimal disease or early relapse following treatment. However, the recently developed ability to detect the Ph chromosome as a rearrangement in the bcr gene of chromosome 22 permits identification of the leukemic clone comprising as little as 5% of the cell population. We present results of simultaneous cytogenetic and DNA rearrangement studies in 28 CML patients considered for or treated with bone marrow transplantation. Our results show that the molecular method is significantly more sensitive than the cytogenetic method in the detection of minimal disease Ph-positive clones.