Objective: The aim of this study was to investigate the correlation between different genotypes of CYP2C19, ERCC2 and XRCC1 and clinical indexes of gastroesophageal reflux and hiatal hernia in Xinjiang. Methods: The clinical data of 101 patients with gastroesophageal reflux and hiatal hernia clinically diagnosed by people′s hospital of Xinjiang Uygur Autonomous Region from January 2016 to December 2017 were prospectively studied, and Wilcoxon rank sum test was used to analyze the genotypes and relevant clinical indicators. Results: There was statistically significant difference in the distance of hiatal hernia between patients with CYP2C19 containing A/A homozygous genotype and those with other two genotypes (A/G or G/G) (P<0.05), and there was statistically significant difference in intrabolus pressure (IBP) between patients with G/G homozygous genotype and those with A/G heterozygous genotype (P<0.05). Esophageal sphincter lower esophageal sphincter (LES) residual pressure, LES relaxation rate and percentage of invalid swallowing between patients with ERCC2 containing A/C heterozygous genotype and those with A/A homozygous genotype also has significant statistical difference (P<0.05). The more C contained in the genotype, the lower IBP maximum (on average), and this pattern has statistical significance (P<0.05); There was no statistical difference for all clinical indicators among different XRCC1 genotypes. Conclusions Different genotypes of CYP2C19 and ERCC2 are closely related to the clinical indexes of gastroesophageal reflux and hiatal hernia. CYP2C19 containing A/G or G/G genotype is correlated with gastroesophageal reflux disease (GERD) and the incidence of hiatal hernia. The population containing A/G and G/G genotypes of CYP2C19 may be with a high incidence of hiatal hernia. Homozygous G/G genotype may be a high risk factor for aggravating reflux esophagitis. A/C and C/C genotypes contained in ERCC2 genotype were correlated with the incidence of hiatal hernia. The more C bases contained in ERCC2 genotype, the greater the effect of reducing IBP, indicating that the more C bases contained in ERCC2 genotype may be negatively correlated with the prevalence of hiatal hernia.