It remains controversial whether the distal rectal pouch should be either resected or used for reconstruction in anorectoplasty for the treatment of anorectal malformations (ARMs). Hence the aim of this study was to investigate whether ARMs were associated with a global neuromuscular maldevelopment of the terminal rectum specimens.There were 36 cases of ARMs (25 recto-bulbar fistula and 11 recto-prostatic fistula) and 10 healthy controls. The hematoxylin and eosin and Masson trichrome stain were used to conduct the histologic examination. The immunohistochemistry (IHC) and Western blot were conducted to analyze the neuron-specific enolase (NSE), S-100 protein, interstitial cells of Cajal marker (C-kit) within the rectal specimens in control group and ARM group.The most frequently observed histologic findings in mucosa were inflammation, congestion, eroded, and hemorrhage in the ARM cases. Submucosal inflammation and congestion were the most common submucosal findings in the ARM cases. Disrupted muscularis propria was observed in 60% of ARM cases. Mature ganglionic cells were reduced and muscularis propria showed reduced and patchy positivity for NSE, S-100, and C-kit protein in ARM group compared to that in control group according to IHC. Western blotting showed the expression levels of NSE, S-100, and C-kit were lower in the ARM group than that in the control group (P < .01).Histopathologic and IHC findings suggest that the distal rectal pouch has distinct defects in the neuromusculature. So it suggested that ARMs are abnormally developed tissue and need to be resected for better functional outcomes of the remaining gut.