Hirschsprung disease (HSCR) is a congenital disorder characterized by the absence of intrinsic ganglion cells in the lower intestine. Genetic factors in the pathogenesis of this disease are under active investigation. As core genes in the planar cell polarity pathway, Celsr3 and Fzd3 are believed to play vital roles in the development of the murine enteric nervous system. The potential association of CELSR3 and FZD3 with the development of HSCR in humans, however, is still unknown. We determined the genotypes of eight CELSR3 and FZD3 polymorphisms in 113 patients. Furthermore, target gene sequencing was used to search for rare mutations in the planar cell polarity genes. The mRNA and protein expression of CELSR3 and FZD3 were explored in patients with HSCR. Class III β-tubulin in colon tissue samples was examined to elucidate enteric innervation patterns. We observed a significant association between the FZD3 rs17059206 polymorphism and HSCR susceptibility (p < 0.001). In addition, five rare mutations in CELSR3 were identified in six patients with HSCR. Upregulation of CELSR3 mRNA expression was detected in 80% of aganglionic segments; a similar increase was found for FZD3 protein expression in 81.8% of aganglionic tissues, compared with the ganglionic segments. Immunohistochemical staining on tissue sections revealed obvious excess expression of both molecules in the mucosal layer. The neurite patterns were highly disorganized in the aganglionic bowel segments, with a marked reduction in the prominence of TUJ1 bundles in number, thickness, and length. Our results showed that deregulation of the planar cell polarity genes CELSR3 and FZD3 might disrupt the enteric innervation pattern and consequently contribute to the susceptibility to HSCR. © 2016