Background Variant Philadelphia chromosomes are characterized by the involvement of another chromosome in addition to chromosome 9 or 22. To detect the difference between variant Philadelphia chromosomes positive leukemia and classic Philadelphia chromosomes positive leukemia. And to help diagnose and treat variant Philadelphia chromosomes positive leukemia. Methods In this study, Peripheral blood and bone morrow cell morphology test was used to analysis bone morphology of variant Ph positive patients. Karyotype analysis was used to find out variant Ph chromosomes. Flow cytometry analysis was used for immunology analysis. BCR/ABL was detected by PCR to monitor change of molecular genetics in variant Ph positive patients. Results From 48 patients with Ph positive leukemia, we found out 3 variant Ph positive leukemia. Compared with the classic Ph positive leukemia patients, the hemogram in the variant Ph positive leukemia patients was more variant for presenting hypomyelodysplasia or hyperactive. Compared with classic chronic myeloid leukemia which neutrophilic myelocyte, metamyelocyte and stab granulocyte is increasing in, both the morphological testing of bone marrow cells smear and flow cytometry analysis were indicated that proportion of myeloblast and promyelocyte increased in variant Philadelphia chromosomes leukemia. What’s more, the variant Ph with breakpoint 4q31 was the first report in leukemia patient. Same as the classic Ph positive leukemia patient, formal and effective treatment could prolong the survival of patients with variant Ph positive leukemia. Conclusions Compared with classic Ph positive leukemia, the hemogram was more variant in variant Ph. The myeloid morphology in the patients with variant Ph was more immature than that of in the patients with classic Ph. Reporting new cases of complex variant translocations, which can refer to new breakpoints that can eventually be recurrent and important for the understanding of this leukemia. Formal and effective treatment are necessary for variant Ph positve leukemia.