Background: There is a paucity of literature on the histopathological aspects of congenital pouch colon (CPC) and immunohistochemical (IHC) assessment has not been reported. So we planned to study the histopathological and IHC findings within the spectrum of CPC and compare the findings with the normal colon. Methods: This is a descriptive prospective study on CPC patients. There were 49 cases of CPC (42 males and 7 females) and 13 controls. Histological examination was done using hematoxylin and eosin and Masson trichrome stain. IHC analysis was done with actin, myosin, and desmin antibodies, and neuron-specific enolase and S100 markers for counting ganglionic cells. Results: Histologically, congestion, edema and hemorrhage were seen in mucosa, submucosa, and serosa. Muscle layers were disrupted and divided into bands. An additional muscle coat inside of the muscularis propria was seen in CPC types 1 and 2. Mature ganglionic cells were reduced and muscle layers showed reduced and patchy positivity for smooth muscle actin, myosin, and desmin compared to a normal colon. Conclusions: Histopathological and IHC findings suggest that CPC has distinct defects in the neuromusculature.