Objective：To investigate the susceptibility of four genetic variations of prostate cancer non-coding RNA 1（LncRNA PRNCR1）to the risk and pathological characteristics of gastric cancer. Methods：A total of 300 gastric cancer cases and 300 health controls were enrolled in this case-control study. The Mass-array gene analysis platform was applied to genotype the enrolled participants. Enzyme-linked immunosorbent assay was used to detect the H. pylori infection. Results：There were significant differences of LncRNA PRNCR1 rs16901946 genotypes distribution between the cases and the control group（P=0.018），and the AG（ORadjusted=1.41，95%CI：1.00-1.98，P=0.048），GG（ORadjusted=2.57，95%CI：1.15-5.75，P=0.022）and AG/GG genotype（ORadjusted=1.51，95%CI：1.09-2.09，P=0.014）were associated with increased risk of gastric cancer，respectively. The results of subgroup analysis showed that LncRNA PRNCR1 rs16901946 was associated with the risk of gastric cancer in the subgroup of male（AG/GG vs. AA：ORadjusted=1.82，95% CI：1.23-2.69，P=0.003），and individuals with H. pylori infection（AG/GG vs. AA：ORadjusted=1.83，95%CI：1.16-2.89，P=0.009）. In addition，LncRNA PRNCR1 rs16901946 was associated with risk of cardia cancer（AG/GG vs. AA：ORadjusted=1.58，95% CI：1.10-2.28，P=0.011）. Similarly it was associated with risk of gastric cancer in clinical stage T1-T2（AG/GG vs. AA：ORadjusted=1.88，95%CI：1.18-2.98，P=0.008）but not in T3-T4. Conclusion：This study indicates that LncRNA PRNCR1 rs16901946 is associated with the increased risk of gastric cancer，especially for male and individuals with H. pylori infection.