Chronic myeloid leukemia patients with different BCR-ABL transcripts might respond differently to Imatinib mesylate. This prompted us to study BCR-ABL transcripts in chronic myeloid leukemia (CML) patients and their correlation with response to Imatinib. Eighty-seven chronic phase CML patients (median age, 35 years; range, 13-62 years; M/F, 59:28) were included in this study; 57 patients had received interferon-alpha and/or hydroxyurea, and 30 were previously untreated. All patients received Imatinib mesylate (Gleevec) 400 mg daily. Complete hematological remission rate and major cytogenetic response (CGR) rates were 99% and 72%, respectively. B3a2 transcript was present in 53% of patients, b2a2 in 39%, and both transcripts in 8% of patients. Twenty of 34(59%) patients with b2a2 type achieved complete CGR compared to 15 of 53 (28%) patients with b3a2, p = 0.04. Among 24 patients with minor or no CGR, six (25%) had b2a2 compared to 18 (75%) b3a2 type, p = 0.04. Expression of BCR-ABL/ABL% was higher in b3a2 patients compared to b2a2, p = 0.120. Pre-treatment characteristics-mean spleen size (6.6 vs. 6.4 cm, p = 0.868), mean hemoglobin (G/dl; 12.0 vs. 11.8, p = 0.690), mean WBC count (83 x 10(9) vs. 77 x 10(9)/L, p = 0.923), and mean platelets counts (360x10(9) vs. 340 x 10(9)/L, p = 0.712)-were not significantly different in the b3a2 vs. b2a2 transcripts groups. Our preliminary findings suggest that CML patients with b2a2 BCR-ABL transcript might have higher CGRs to Imatinib mesylate (Gleevec).