Background Hirschsprungs disease (HD) is common congenital gastrointestinal malformation,characterized by the lack of neurons from distal rectum to proximal bowel.Autophagy, a conserved lysosomal degradation pathway, modulates neural cell differentiation and degeneration in central nervous system.But it is not clear if autophagy is involved in hirschsprungs disease.Method In this study we used electron miscroscope to ditect the autophagosome in different segments of the bowel from hischsprung disease.Real-time PCR and immunohistochemical staining were used to exam the expression levels of Beclin1 and LC3 in different segments.Results We observed typical autophagosome structures in Auerbach plexes of both narrow and transitional segments.Beclin1 and LC3 mRNA levels were found highest expression in narrow segments.And we observed positive correlation between Beclin1 and LC3 mRNA levels.Immunohistochemistry analyses indicated increased Beclin1 and LC3 protein levels in Auerbach plexes of narrow segments, a result consistent with the mRNA levels.Conclusions These findings have for the first time revealed that autophagy existed in the bowel of Hirschsprungs disease.Based on the detection of highest expression of the genes associated with autophagy, autophagy may cause the lack of neurons.This results may contribute to clarify the mechnism of Hirschsprungs disease.