Recent genome-wide association studies (GWAS) have identified more than 200 regions that affect susceptibility to inflammatory bowel disease (IBD). However, identified common variants account for only a fraction of IBD heritability and have largely been identified in populations of European ancestry. We performed a GWAS of susceptibility loci in Korean individuals, comprising a total of 1,505 IBD patients and 4,041 controls. We identified 2 new susceptibility loci for IBD at genome-wide significance: rs3766920 near PYGO2-SHC1 at 1q21 and rs16953946 in CDYL2 at 16q23.