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Purpose: Recent genome-wide association studies have identified a number of inflammatory bowel diseases (IBD) susceptibility loci in White populations. The aim of our study was to evaluate whether these susceptibility loci also existed in a Chinese Han IBD population. Methods: Peripheral blood DNA samples from groups of patients with Crohn's disease (CD) ( n = 48), ulcerative colitis (UC) ( n = 49), and healthy controls ( n = 50) were genotyped for eight genes. Then, an extended analysis of the relationship between genotype and phenotype was performed. Results: NOD2-P268S ( P = 0.025) was found to contribute susceptibility to CD in the Chinese population. IL23R-rs11805303 was detected to confer a strong protective effect against UC ( P = 0.010), whereas PTPN2-rs2542151 was significantly associated with an increased risk of UC ( P = 0.001). Further phenotype-genotype analysis revealed that P268S was associated with early age of onset ( P = 0.028), ileal disease ( P = 0.003), and enteric cavity narrowing ( P = 0.007). Conclusions: The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute to the development of UC and NOD2-P268S might be involved in the etiology of CD in the Chinese Han population. [ABSTRACT FROM AUTHOR]