Objective To evaluate the diagnostic and prognostic significance of 43 fusion gene screening in combination with immunophenotyping and cytogenetics in childhood hematologic neoplasms. Methods A total of 176 children from Shanghai Children′s hospital with acute leukemia newly or recurrently diagnosed from May.2015 to Apr.2017 were enrolled into this study.There were 99 males and 77 females,aged between 4 months to 15 years old.Application of real-time fluorescent probe PCR assay for detection of 43 fusion genes including the common type of BCR-ABL,AML1-ETO, CBFβ-MYH11, MLL and RaRα related fusion genes in ALL(Acute lymphoblastic leukemia)and AML(Acute myeloid leukemia).Results The fusion genes were detected at positive rate of 28.4 %(50/176).The final diagnosis included 110 cases of ALL-B,11 cases of ALL-T and 46 cases of AML,the other 9 cases were as follows:1case of neuroblastoma,2 cases of NHL -B,1case of NHL -T,1case of AML transformed from CML,2 cases of M DS,1 case of CML and 1 case of anemia.Positive fusion gene of ALL -B(27/110, the positive rate of 24.5%),included:TEL-AML1 14 cases,E2A-PBX1 6,MLL-AF10 2 and MLL -AF4 2,MLL-AF9 1,MLL -ENL 1 and BCR-ABL 1 cases.ALL -T positive rate 27.3%(3/11):1 case with MLL-ENL and 2 cases of SIL -TAL1.In AML patients the positive rate was 37%(17/46), included AML-ETO 7,MLL -AF10 1, MLL -AF10 1, PML-RaRa 4, DCK -CAN 3and CBFB -MYH11 1 case respectively.The other included BCR-ABL 2 cases, E2A-PBX1 1 case.Conclusion The 43 fusion gene screening contribute to leukemia diagnosis and differential diagnosis, which helps to evaluate the risk stratification and prognosis effectively.