Hirschsprung disease (HSCR) is a genetic disorder characterized by the absence of neural crest cells in parts of the intestine. This study aims to investigate the association of vesicle-associated membrane protein 5 ( ) and mutated in colorectal cancer ( ) genetic polymorphisms and their correlated risks with HSCR. We examined the association in four polymorphisms (rs10206961, rs1254900 and rs14242 in , rs11241200 in ) and HSCR susceptibility in a Southern Chinese population composed of 1473 cases and 1469 controls. Two variants in were replicated as associated with HSCR. Interestingly, we clarified SNPs rs10206961 and rs1254900 in are more essential for patients with long-segment aganglionosis (LHSCR). Relatively high expression correlation was observed between and using data from public database showing there may exist potential genetic interactions. SNP interaction was cross-examined by logistic regression and multifactor dimensionality reduction analysis revealing that rs1254900 and rs11241200 were interacting significantly, thereby contributing to the risk of HSCR. The results suggest that significant associations of the rs10206961 and rs14242 in with an increased risk of HSCR in Southern Chinese, especially in LHSCR patients. This study provided new evidence of epistatic association of and with increased risk of HSCR.