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Background: Acute graft?versus?host disease (aGVHD) is a common and severe complication of allogeneic hematopoietic stem cell transplantation (allo?HSCT). Some studies have found that the presence of certain specific human leukocyte antigen (HLA) loci could affect the occurrence of aGVHD. Meanwhile, the impact of HLA haplotypes on aGVHD has been rarely studied. This study aimed to investigate the effects of HLA loci and haplotypes on intestinal aGVHD. Methods: Totally, 345 consecutive patients undergoing first HLA?matched sibling peripheral blood stem cell transplantation (PBSCT) from February 2004 to June 2013 at Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, were enrolled in this study. HLA loci and haplotypes of recipients with frequency over 5% were searched and their effects on intestinal aGVHD were investigated. Other important factors including donor age, recipient age, donor?recipient sex combinations, and conditioning regimens were also evaluated using logistic regression. Pure upper gastrointestinal tract aGVHD without diarrhea was excluded because the histological proof was unavailable. The follow?up end?point was 6 months after HSCT. Results:The cumulative incidence of intestinal aGVHD was 19.4%,with 18.0%of the patients classified as classic aGVHD and 1.4% aspersistent, recurrent,or late aGVHD.Multivariate analysis showed that HLA?A31 locus(odds ratio[OR]2.893,95% confidence interval[CI][1.054,7.935], P = 0.039), HLAB40?DR15 (OR 3.133, 95% CI [1.250, 7.857], P = 0.015), and HLAB46?DR9 haplotypes (OR 2.580, 95% CI [1.070, 6.220], P = 0.035), female donor for male recipient (OR 2.434, 95% CI [1.319, 4.493], P = 0.004) were risk factors for intestinal aGVHD. Conclusion: The presence of certain HLA loci and haplotypes may influence the occurrence of intestinal aGVHD in PBSCT with HLA?identical sibling donors.