Objective To investigate the influence of single nucleotide polymorphism (SNP) of methylenetetrahydrofolate reductase (MTHFR) and thiopurine S-methyltransferase (TPMT) on adverse reactions of chemotherapy in children patients with acute lymphocytic leukemia (ALL).Methods Ninety-eight children patients withALL in the pediatric department of this hospital from Jan.2014 to Dec.2016 were chosen.The gradient PCR and DNA sequencing were adopted to detect the genotypes of MTHFR C677T,A1298C and TPMT A719G,G460A.The relationships between different SNP with adverse reactions were compared.Results The mutauon rates of MTHFR C677T and A1298C were 66.33％ and 44.90％ respectively,which of TPMT A719G and G460A were 12.24％ and 9.18％ respectively.The proportion of MTHFR A1298AC developing thrombocytopenia was 28.13％,which was higher than 7.41％ of those carrying A1298AA and 8.33％ of those carrying A1298CC,the difference was statistically significant (P＜0.05).The proportion of MTHFR carrying A1298AA developing mucosal injury was 9.26 ％,which was lower than 43.75％ of those carrying A1298AC and 50.00％ of those A1298CC (P＜0.05).The differences in the genotypes of MTHFR C677T,TPMT A719G and TPMT G460A and the adverse reactions after chemotherapy were not statistically significant (P＞0.05).Conclusion The MTHFR A1298C polymorphism might be associated with the adverse reactions of MTX chemotherapy in ALL children.