Homozygosity for a nonsense mutation in the fucosyltransferase 2 (FUT2) gene (rs601338G>A) leads to the absence of ABH blood groups (FUT2 non-secretor status) in body fluids. As the secretor status has been shown to be a major determinant for the gut microbial spectrum, assumed to be important in the gut immune homeostasis, we studied the association of rs601338-FUT2 with celiac disease (CelD) and inflammatory bowel disease (IBD) in the Finnish population. Rs601338 was genotyped in CelD (n?=?909), dermatitis herpetiformis (DH) (n?=?116), ulcerative colitis (UC) (n?=?496) and Crohn's disease (CD) (n?=?280) patients and healthy controls (n?=?2738). CelD showed significant genotypic [P?=?0.0074, odds ratio (OR): 1.28] and recessive (P?=?0.015, OR: 1.28) association with the rs601338-AA genotype. This was also found in the combined CelD+DH dataset (genotype association: P?=?0.0060, OR: 1.28; recessive association: P?