Different BCR-ABL transcript variants occur more or less frequently, according to the leukemia type. We report the frequencies of BCR-ABL transcript variants studied in chronic myeloid leukemia (CML) and acute lymphoblastic leukemia (ALL) patients in the Ecuadorian population. The frequencies found for CML patients in this study were 94.6% for the b2/a2 rearrangement and 5.4% for the b3/a2 rearrangement; whereas in ALL, all cases (100%) that presented the BCR-ABL rearrangement had the e1/a2 junction. Since our results differ from the frequencies previously reported, we suggest that this may be due to a different genetic background in the population involved in this study when compared to the populations analyzed in prior studies. Furthermore, we recommend a survey of the BCR-ABL transcript variants and their frequencies in different ethnic groups.