Objective Hirschsprung disease (HSCR) originates from disruption of normal neural crest cell migration, differentiation, and proliferation during the fifth to eighth weeks of gestation. This results in the absence of intestinal ganglion cells in the distal intestinal tract. However, genetic variations affecting embryonic development of intestinal ganglion cells are unclear. Therefore, this study aimed to investigated the potential value of miR-492 rs2289030 G>C as a marker of susceptibility to HSCR Methods In this case–control study in southern Chinese children, we collected samples from 1473 controls and 1470 patients with HSCR. TaqMan genotyping of miR-492 rs2289030 G>C was performed by real-time fluorescent quantitative polymerase chain reaction. Results Multivariate logistic regression analysis showed that there was no significant association between the presence of the miR-492 rs2289030 G>C polymorphism and susceptibility to HSCR by evaluating the values of pooled odds ratios and 95% confidence intervals. Similarly, among different HSCR subtypes, rs2289030 G>C was also not associated with HSCR in hierarchical analysis. Conclusions Our results suggest that the miR-492 rs2289030 G>C polymorphism is not associated with susceptibility to HSCR in southern Chinese children. These results need to be further confirmed by investigating a more diverse ethnic population of patients with HSCR.