The study aimed to examine a rare case of Philadelphia (Ph)-negative chronic myeloid leukemia (CML) with t(9;13). Chromosome samples were prepared after culture of bone marrow cells for 24 hours, the karyotypes were analyzed by G banding technique. Chromosome painting analysis was performed by using whole chromosome paints for chromosomes 9 and 22. Fluorescence in situ hybridization (FISH) was done with dual color dual fusion LSI bcr/abl probe. Bcr/abl transcripts were detected by real time fluorescence quantitative polymerase chain reaction (RQ-PCR). As a result, G banding analysis showed a karyotype of 45, XX, der(9)t(9;13)(q34;q10), -13[20]. FISH assay using LSI bcr/abl DNA probe showed a red abl signal inserted into der(22) and a fusion signal of bcr/abl rearrangement was discovered. RQ-PCR detected high copies of bcr/abl transcripts. In conclusion, insertion of bcr/abl rearrangement was a rare variant t(9;22) and could be well detected by molecular techniques, however, regular cytogenetic banding technique and whole chromosome paintings may probably lead a misdiagnosis to such cases.