Mucosal addressin cell adhesion molecule-1 (MAdCAM-1) contributes to the recruitment of donor T cells into the mucosal tissues of the recipient after allogeneic hematopoietic stem cell transplantation (aHSCT). The aim of our study was to determine whether selected single nucleotide polymorphisms (SNPs) of the MADCAM1 gene are associated with development of serious complications after aHSCT. Three MADCAM1 gene single nucleotide polymorphisms (rs758502 C/T, rs2302217 A/G, rs3745925 G/T) were genotyped by polymerase chain reaction with sequence-specific primers in 87 Czech, HLA-identical donor-recipient aHSCT pairs. MADCAM1 rs2302217 AA homozygous recipients developed chronic GVHD more frequently than patients with other genotypes (65% vs. 34%; p = 0.025). Furthermore, multivariate analysis revealed the MADCAM1 rs2302217 AA genotype in recipient being also an independent factor associated with development of acute GVHD (p = 0.036) and decreased overall survival (p = 0.001). These data suggest that MADCAM1 gene polymorphisms may be associated with the risk of chronic GVHD and may, also, affect mortality related to aHSCT.