Background: Different BCR-ABL fusion transcripts occur more or less frequently, in three different types of leukemia Objectives: This study was done to determine the frequencies of BCR-ABL fusion transcripts in leukemia patients from Iran. Methods: This experimental study was carried out from 2001 to 2015 in Pasteur Institute of Iran. The leukemia patients containing 348 chronic myeloid leukemia (CML), 72 acute lymphoblastic leukemia (ALL), and 34 acute myeloid leukemia (AML) were studied. Total RNA was extracted from peripheral blood samples and analyzed by multiplex RT-PCR in 486 leukemia patients to detect different types of BCR-ABL transcripts. Fisher's exact test was used in comparing qualitative variables in the case control study. Associations with a P value < 0.05 were considered significant. Results: The BCR-ABL transcript frequencies for CML, ALL and AML patients were 92.0%, 12.5% and 14.7% respectively for all transcripts. The majority of CML patients with positive BCR-ABL expressed one of the p210 BCR-ABL transcripts (86.6%) while the remaining showed