Abstract： Objective To explore the relationship between exon 3 mutation in the methyl CpGbinding protein 2 (MeCP2-E3) gene and Hirschsprung disease (HSCR) and anorectal malformations (ARMs).Methods PCR and DNA sequencing were used to detect the mutation of MeCP2-E3 in 120 healthy controls,120 HSCR,and 50 ARMs.Results On sequencing,45(37.5％) children with HSCR had basic replacement in MeCP2-E3,12 (10.0％) of them were homozygous mutation.Fourteen(28.0％) children with ARMs had basic replacement in MeCP2-E3,4(8％) of them were homozygous mutation.There were no mutation in the control group.Conclusions Mutation of MeCP2E3 is present in the peripheral blood of children with HSCR or ARMs,which may contribute to the development of Hirschsprung disease or anorectal malformations.