The addition of imatinib to high-intensity chemotherapy has improved the outcome of patients with Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL). However, the possible long-term side effects of this combination are not yet known. Development of new clonal abnormalities in complete cytogenetic remission after treatment with imatinib has been reported in patients with chronic myeloid leukemia but not in patients with Ph-positive ALL. Here, we present a patient with Ph-positive ALL who received hyperCVAD plus imatinib and achieved hematologic, cytogenetic, and major molecular responses. The patient then developed myelodysplastic syndrome and solitary central nervous system relapse of ALL.