Aims: The goal of our study is to investigate the contribution of the 13 single-nucleotide polymorphisms to inflammatory bowel disease (IBD), including Crohn's disease (CD) and Ulcerative colitis (UC). Methods: A total of 44 articles were retrieved from bibliographic databases including PubMed, Embase, SpingerLink, Web of Science, Chinese National Knowledge Infrastructure (CNKI), and Wanfang. Through a comprehensive filtering procedure, 13 single-nucleotide polymorphisms were collected in the meta-analysis, which was done by Review Manager 5.0. Results: After a systematic filtration, there were 13 single-nucleotide polymorphisms (SNPs) from 44 articles involved in our meta-analysis. Our results demonstrated that 3 SNPs were found to be significantly associated with CD/UC/IBD: IRF5 rs4728142 (UC: OR = 1.21, 95% CI = 1.09-1.35, P = 0.0003; OR = 1.30, 95% CI = 1.08-1.57, P = 0.006 in Asian), PTGER4 rs4613763 (CD: the overall OR = 1.28, 95% CI = 1.01-1.64, P = 0.04; IBD: OR = 1.31, 95% CI = 1.04-1.65, P = 0.02), IL12B rs6887695 (CD: the overall OR = 1.17, 95% CI = 1.06-1.30, P = 0.002; UC: the overall OR = 1.13, 95% CI = 1.01-1.26, P = 0.03; IBD: the overall OR = 1.15, 95% CI = 1.06-1.24, P = 0.0009). Conclusion: Our meta-analyses have indicated the significant associations between SNPs (IRF5 rs4728142, PTGER4 rs4613763, and IL12B rs6887695) and CD/UC/IBD.