BACKGROUND: Reactive arthritis (ReA) is a recognized sequela of infectious gastroenteritis (IGE). However, the population-based incidence of IGE-related ReA is poorly defined, and the risk of disease has not previously been characterized in a military population. The intent of this study was to provide estimates of the incidence and morbidity associated with IGE-related ReA in the U.S. military population. METHODS: Using active duty US military medical encounter data from the Defense Medical Surveillance System, we conducted a matched case-control study to assess the risk of ReA following IGE. Both specific and nonspecific case definitions were utilized to address ICD-9 coding limitations; these included specific ReA (Reiter's Disease or postdysenteric arthritis) and nonspecific arthritis/arthralgia (N.A.A) (which included several related arthropathy and arthralgia diagnoses). Incidence was estimated using events and the total number of active duty personnel for each year. RESULTS: 506 cases of specific ReA were identified in active duty personnel between 1999 and 2007. Another 16,365 cases of N.A.A. were identified. Overall incidence was 4.1 (95% CI: 3.7, 4.5) and 132.0 (95% CI, 130.0-134.0) per 100,000 for specific ReA and N.A.A, respectively. Compared to the youngest age category, the incidence of both outcomes increased 7-fold with a concurrent increase in symptom duration for cases over the age of 40. Specific IGE exposures were documented in 1.4% of subjects. After adjusting for potential confounders, there was a significant association between IGE and ReA (specific reactive arthritis OR: 4.42, 95% CI: 2.24, 8.73; N.A.A OR: 1.76, 95% CI: 1.49, 2.07). CONCLUSIONS: Reactive arthritis may be more common in military populations than previously described. The burden of ReA and strong association with antecedent IGE warrants continued IGE prevention efforts.