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Background Crohn's disease ( CD) and ulcerative colitis ( UC) are two pathotypes of inflammatory bowel disease ( IBD) with unique pathology, risk factors and significant morbidity. Aim To estimate incidence and identify IBD risk factors in a US military population, a healthy subset of the US population, using information from the Millennium Cohort Study. Methods Incident IBD was identified from medical encounters from 2001 to 2009 or by self-report. Our primary risk factor of interest, infectious gastroenteritis, was identified from medical encounters and self-reported post-deployment health assessments. Other potential risk factors were assessed using self-reported survey responses and military personnel files. Hazard ratios were estimated using Cox proportional hazards analysis. Results We estimated 23.2 and 21.9 diagnoses per 100 000 person-years, respectively, for CD and UC. For CD, significant risk factors included [adjusted hazard ratio ( aHR), 95% confidence interval]: current smoking ( aHR: 2.7, 1.4-5.1), two life stressors ( aHR: 2.8, 1.4-5.6) and prior irritable bowel syndrome ( aHR: 4.7, 1.5-15.2). There was no significant association with prior infectious gastroenteritis. There was an apparent dose-response relationship between UC risk and an increasing number of life stressors. In addition, antecedent infectious gastroenteritis was associated with almost a three-fold increase in UC risk ( aHR: 2.9, 1.4-6.0). Moderate alcohol consumption ( aHR: 0.4, 0.2-0.6) was associated with lower UC risk. Conclusions Stressful conditions and the high risk of infectious gastroenteritis in deployment operations may play a role in the development of IBD in military populations. However, observed differences in risk factors for UC and CD warrant further investigation. [ABSTRACT FROM AUTHOR]