Although inflammatory bowel diseases (IBD) is presumed to develop as the result of dysregulated immune response to the intestinal microbiota in genetically susceptible hosts, the association between microbiota and genotypes in IBD patients remains unclear. The human leukocyte antigen (HLA)-Cw*1202-B*5201-DRB1*1502 haplotype has been reported to increase the susceptibility to ulcerative colitis (UC), but reduce the risk of Crohn’s disease (CD). We investigated the association between HLA genotype and mucosal microbial composition to elucidate factors that might affect disease phenotypes among IBD patients.