Objectives: The aim of this study was to assess the risk of incident rheumatological diagnoses (RD) associated with self-reported diarrhoea and vomiting during a first-time deployment to Iraq or Afghanistan. Such an association would provide evidence that RD in this population may include individuals with reactive arthritis (ReA) from deployment-related infectious gastroenteritis. Design: This case-control epidemiological study used univariate and multivariate logistic regression to compare the odds of self-reported diarrhoea/vomiting among deployed US military personnel with incident RD to the odds of diarrhoea/vomiting among a control population. Setting: We analysed health records of personnel deployed to Iraq or Afghanistan, including responses on a postdeployment health assessment and medical followup postdeployment. Participants: Anonymous data were obtained from 891 US military personnel with at least 6 months of medical follow-up following a first-time deployment to Iraq or Afghanistan in 2008-2009. Cases were defined using International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) diagnosis codes; controls had an unrelated medical encounter and were representative of the study population. Main outcome measures: The primary measure was an association between incident RD and self-reported diarrhoea/vomiting during deployment. A secondary measure was the overall incidence of RD in this population. Results: We identified 98 cases of new onset RD, with a total incidence of 161/100 000 persons. Of those, two participants had been diagnosed with Reiter's diseasei (3.3/100 000 persons) and the remainder with nonspecific arthritis/arthralgia (157.5/100 000 persons). The OR for acute diarrhoea was 2.67 (p=0.03) after adjusting for important covariates.