The Joint Medical Work Station (JMeWS) is a theater medical surveillance system that integrates information from three separate health data collection systems for the Army, Navy, Air Force, and Marines. Our objective was to characterize JMeWS data during its first year of implementation in 2003. We conducted a descriptive analysis of health events documented in JMeWS among military personnel deployed to Operations Enduring Freedom and Iraqi Freedom. Among the 38,498 individuals (7.8%) with a JMeWS record, women, college-educated, older individuals, and Reserve/Guard personnel were over-represented. There was wide variability by service (Air Force, 25%; Army, 5.5%; Marine Corps, 1.2%; and Navy, 0.6%). The most common diagnoses were in the categories of injury and poisoning, respiratory conditions, and musculoskeletal disorders. Differences in distribution of the various patient encounter modules in theater likely resulted in variable data capture across services. System enhancements should improve future applications.