Little evidence exists regarding the prognostic impact of the major BCR-ABL gene variants (e13a2 and e14a2) in chronic myeloid leukemia (CML) patients diagnosed and treated in the developing Asian countries. In this study, 139 Thai CML patients were followed for a median period of 3 years (range 18-43 months). Clinical presentations of both BCR-ABL gene variant groups (73% e14a2+ and 27% e13a2+) were similar, although e14a2+ patients tended to be older (42 vs. 37 years) and had higher white blood cell counts than e13a2+ patients. The majority of patients in both groups presented with Sokal stage 2-3 (score >0.8) and were categorized as Hasford's intermediate- to high-risk groups (score >780). All patients received oral chemotherapy and 13% underwent allogeneic stem cell transplantation. None received oral tyrosine kinase inhibitors. In the conventional chemotherapy group, the overall survival (OS) rate was slightly better in e14a2+ than in e13a2+ patients (p = n.s.). The median survival in e14a2+ and e13a2+ patients who did not receive stem cell transplantation was 49 and 33 months, respectively (p = n.s.). The type of blastic crisis in e14a2+ and e13a2+ patients was similar, being predominantly myeloid. In conclusion, CML patients in Thailand, despite being much younger, had a comparable OS with those in the Western countries, with no different OS between e14a2+ and e13a2+ patients. Future studies should focus on the impact of novel oral BCR-ABL tyrosine kinase inhibitors on the outcome of Thai CML patients with different BCR-ABL gene variants.