This study was aimed to compare the curative effect of BCH - 2003 protocol and CCLG - 2008 protocol for children with TEL-AML1 fusion gene positive childhood acute lymphoblastic leukemia (ALL) and to investigate the more suitable protocol for this subtype of childhood leukemia. The clinical data for children with TEL-AML1 fusion gene positive ALL admitted from January 2003 to October 2010 in Hematology Center of Beijing Children's Hospital were collected. The common clinical characteristics including prednisone response at day 8, minimal residual disease (MRD) at the end of induction of remission (day 33), event free survival (EFS), relapse free survival (RFS) were compared. The results showed that out of 204 children with TEL-AML1 fusion gene positive ALL, 134 and 70 patients were treated by BCH-2003 protocol and CCLG-2008 protocol respectively. There were no statistical difference in age, white blood cell count in peripheral blood at presentation, prednisone response and CNS involvement. However, there were more boys in CCLG-2008 group (P = 0.025). The negative rate of MRD at day 33 in BCH-2003 group was lower than that in CCLG-2008 group (P = 0.013). After re-stratifying the patients in CCLG-2008 group according to the stratification criteria of BCH-2003 protocol, the negative rate of MRD at day 33 of patients with intermediate risk remained higher in BCH-2003 group than that in CCLG-2008 group (P = 0.014) . However, no significant difference in the patients with standard risk was found. There were also no significant statistical differences in the incidence of severe infection, EFS and RFS, (P = 1.000, P = 0.327,P = 0.251 respectively) during chemotherapy. It is concluded that for children with TEL-AML1 fusion gene positive ALL, the induction of remission of BCH - 2003 protocol can decrease leukemic load more quickly than that of CCLG - 2008 protocol. However, the outcome of the patients treated by the two protocols is similar.