OBJECTIVE: To study the Hoxd 13 gene expression in the children with anorectal malformation (CAM) and normal children, and to explore the relationship between Hoxd 13 gene and CAM. METHODS: Hoxd 13 gene mRNA expression was detected by RT-PCR in the rectal pouch in both 16 cases of anorectal malformations and 5 normal children. RESULTS: The expression level of Hoxd 13 gene mRNA was significantly higher in normal children than that in children with CAM ( 0.32 ± 0.26 vs 0.73 ± 0.10 ), (P< 0.01 ). CONCLUSIONS: Hoxd 13 gene expression may be involved in the pathogenesis of anorectal malformation.