Diarrhoea and vomiting (D & V) was common in military personnel during deployment to the initial phases of the Iraq war. D & V is an established risk factor for irritable bowel syndrome (IBS). This study examined the prevalence of IBS in a military sample with a history of deployment to Iraq and the association between D & V and common mental disorder (CMD) with IBS. Methods The study used data from a two-phase cohort study of military/personnel. The sample was restricted to individuals who had been deployed to Iraq before phase 1 of the study and who had completed the self-report D & V question. A measure of probable IBS was derived at both phases of the study based on self-reported symptoms in the previous month. CMD was assessed by the General Health Questionnaire (GHQ-12). Results Fifty-nine percent of the sample reported a D & V event and 6.6 % met the criteria for probable IBS at phase 1. Reporting D & V, thinking one might be killed on deployment, poor physical health and CMD were associated with probable IBS at phase 1. CMD at phase 1 was strongly associated with chronic symptoms of IBS. Conclusions There was a high prevalence of D & V during deployment to the early stages of the Iraq war, yet the prevalence of probable IBS on return from deployment was relatively low. D & V was strongly associated with IBS after deployment, and CMD was a risk factor for chronic symptoms of IBS.