Objective To study methylation status of the Runx3 gene in occurrence and development of children malignant lymphoma.Methods The bone marrow specimens of 48 children diagnosed as malignant lymphoma were included into experimental group.20 children with non-malignancy were included into control group.Methylation-specific polymerase chain reaction (MS-PCR) was used to detect methylation status of Runx3 gene in bone marrow cells.The reverse transcription-polymerase chain reaction (RT-PCR) was used to detect mRNA expression of Runx3 gene.Results MS-PCR assay results showed that 31 cases expressed Runx3 gene methylation in experimental group,the positive rate was 64.6 ％ (31/48),but no one was detected in control group (20 cases),the difference between two groups was significant (x2 =15.7,P ＜0.05).Dynamic observation of 42 cases in experimental group showed the declining of Runx3 methylation positive rate.RT-PCR assay results showed that all 20 cases in the control group expressed Runx3 gene mRNA,all cases with methylation status of the Runx3 gene in the experimental group didn’ t expressed Runx3 gene mRNA.In experimental group,9 cases of clinical remission expressed Runx3 gene mRNA,and 1 case of relapsed didn’ t expressed Runx3 gene mRNA.Conclusion Runx3 gene shows a high methylation status in bone marrow cells of malignant lymphoma children,so that blocked the expression of Runx3 gene,which is closely related to the occurrence and development of children malignant lymphoma.