We report a patient who developed a bone and adjacent soft tissue malignancy 22 months after bone marrow transplantation (BMT) for Philadelphia chromosome positive chronic myelogenous leukemia (CML). Concomitant bone marrow was cytologically and cytogenetically normal. Cytogenetic study of tumoral tissue was unsuccessful but DNA analysis revealed BCR-AB1 rearrangement similar to that observed in hematopoietic cells prior to BMT. The present case demonstrates that molecular analysis is helpful in the diagnosis of unusual relapse of CML.