BACKGROUND Five to 10% of patients with chronic myelogenous leukemia (CML) do not have the Philadelphia chromosome (Ph), but one-third of them have rearrangements of the breakpoint cluster region (BCR-positive). METHODS The authors analyzed the characteristics, treatment response, and prognosis of 23 patients with BCR-positive, Ph-negative CML, and compared them with patients with Ph-positive CML, Ph-negative BCR-negative CML and chronic myelomonocytic leukemia (CMML) treated during the same period. RESULTS Seventeen patients had early chronic phase CML, 3 had late chronic phase, 2 had accelerated phase, and 1 had blastic phase. The median age was 44 years (range, 14-71 years), median platelet count was 402 x 10(9)/l, and median leukocyte count was 86 x 10(9)/l. Fourteen of the 17 patients with early chronic phase CML received alpha-interferon; 12 (86%) achieved complete hematologic remission. Median survival in chronic phase CML was 60 months (range, 3-90+ months). Patients with Ph-negative BCR-positive CML and those with Ph-positive CML had similar characteristics and outcome. Compared with patients with Ph-negative BCR-negative CML and CMML, patients with Ph-negative BCR-positive CML and Ph-positive CML were significantly younger, had a significantly higher incidence of leukocytosis, thrombocytosis, and peripheral and marrow basophilia, and a significantly lower incidence of anemia, thrombocytopenia, marrow blast percent, and peripheral and marrow monocytosis. The median survival was 60 months for Ph-negative BCR-positive CML, 73 months for Ph-positive CML, 25 months for Ph-negative BCR-negative CML, and 9 months for CMML (P < 0.001). When analyzed adjusting for their stage, patients classified with Ph-negative BCR-positive CML. Stage I disease had a significantly better survival than did patients with Ph-negative BCR-negative CML (P < 0.02). CONCLUSIONS Patients with Ph-negative BCR-positive CML are similar to those with Ph-positive CML and should be treated with the same approaches.