The Philadelphia chromosome (Ph) is the cytogenetic hallmark of chronic myeloid leukemia (CML) and as such has been used to confirm the diagnosis of CML based on morphological and clinical criteria. We have investigated 12 patients who were considered to have clinical and morphological features of CML and who did not have detectable abnormalities of chromosomes 9q34 or 22q11. In six of the 12 patients, rearrangement within the 5.8 kb major breakpoint region (M-bcr) and amplification of CML specific M-bcr-ABL cDNA sequences by the polymerase chain reaction (PCR) was demonstrated. Six other CML patients did not have rearrangement of the M-bcr gene or amplification of BCR-ABL by PCR. These patients had atypical CML. They were significantly older, most had less than 10% immature granulocytic cells (metamyelocytes, myelocytes and promyelocytes) and had various degrees of marrow fibrosis. Three of these six patients died of blastic transformation at 4, 15 and 54 months from diagnosis.