The bcr gene rearrangement resulting from the Philadelphia translocation is diagnostic of chronic myelogenous leukemia (CML) and is considered the hallmark of this myeloproliferative disorder (MPD) at the molecular level. The other MPDs, essential thrombocythemia (ET), polycythemia vera (PV), agnogenic myeloid metaplasia (AMM), and unclassified MPD, share morphologic features with CML, making the diagnosis difficult in cases with considerable morphologic overlap. In such cases, molecular analysis becomes essential for accurate diagnosis. We report results of bcr analysis by Southern hybridization in 37 patients with MPDs other than CML: ET (20 cases), PV (seven cases). unclassified MPD (nine cases), as well as in one case of chronic myelomonocytic leukemia (CMML). bcr negativity ruled out CML in 36 cases, confirming the morphologic diagnosis. In one case diagnosed as ET. bcr gene rearrangement was diagnostic of CML. The correct diagnosis made possible a different therapeutic approach in this young patient and resulted in cure after allogeneic bone marrow transplantation. The existence of such cases makes the use of molecular analysis essential in the evaluation of MPDs, even when the morphologic features do not unequivocally support the diagnosis of CML, as in this patient.