One of the widely accepted hypotheses of Hirschsprung’s disease (HD) is that the absence of ganglion cells in the distal part of the intestine is caused by the death of enteric neural crest-derived cells following migration. Although a caspase-dependent pathway has not yet been detected in the HD bowel, it is unclear whether a caspase-independent pathway contributes toward aganglionosis. In the current study, we observed highly condensed marginal heterochromatin in nuclei only in the transitional segment using electron microscopy and a high proportion of TUNEL-positive cells were observed in the transitional segment. Activation of caspase was not observed in any segments of the HD bowel upon characterization of the apoptotic pathway. Rather, real-time PCR results showed that apoptosis-inducing factor (AIF) and calpain-1 mRNAs were highly expressed in the transitional segment, whereas autophagy protein 5 (Atg5) was highly expressed in the narrow segment. Western blot results were consistent with mRNA levels, with increased AIF, calpain-1, and Atg5 expressions in the transitional segment compared with the dilated segment. Furthermore, correlation analysis indicated an inverse correlation between calpain-1 and Atg5 mRNA levels in both the narrow segment and the transitional segment. These results indicated that apoptosis occurs in the HD bowel. The detection of related genes indicates that the AIF-mediated apoptotic pathway may be responsible for the absence of ganglion cells in HD and calpain-1 may act as the regulatory switch between autophagy and apoptosis.