In this report, we describe a rare 5q--/CML association in a patient with Ph-positive chronic myelogenous leukemia (CML) who achieved complete cytogenetic response on interferon-alpha (IFN-alpha) treatment, but who developed a new clone in the blastic crisis. The patient was treated with interferon-alpha beginning in 1996 and a serial chromosome and molecular study was performed over the clinical course of the disease. The patient remained in complete hematologic and cytogenetic remission until November 1998, when a reverse transcriptase PCR study performed on the bone marrow and peripheral blood cells was negative for chimeric BCR/ABL mRNA. The treatment was discontinued until April 1999, when the patient developed acute transformation of the disease. In June 1999, cytogenetic examination showed the development of a new clone, consisting of the deletion of the long arm of chromosome 5 in addition to the standard Ph translocation. The unusual association of a Ph with an abnormality usually observed in a secondary myeloproliferative disease raises the question of whether the new finding is treatment-induced or part of the disease process and casually related to the acute transformation.