The present invention provides a method of determining a risk of pouchitis development following a surgical procedure where an internal pouch is created in a patient with ulcerative colitis. The method is practiced by determining in the patient the presence or absence of a pouchitis-associated allele linked to an interferon .gamma. receptor locus, where the presence of the pouchitis-associated allele indicates an increased risk of pouchitis development. The interferon .gamma. receptor locus to which the pouchitis-associated allele is linked can be, for example, an interferon .gamma. receptor 1 gene. A pouchitis-associated allele useful in the invention can be, for example, an allele located within the sixth intron of the interferon .gamma. receptor 1 gene, such as a FA1 microsatellite 171 allele.