The purpose of this study was to investigate the relationship between back, neck, and upper extremity (UE) musculoskeletal pain and the wear of individual body armor, physical training (PT), and work tasks. We conducted a cross-sectional randomized-survey design in which 1,187 surveys were distributed to U.S. Soldiers in Iraq; 863 were completed. The survey was a three-page questionnaire covering demographics, body armor wear, PT, and reports of neck, back, and UE musculoskeletal pain before and during deployment. The results of the survey revealed a substantial increase in the incidence of back, neck, and UE pain during deployment, and approximately twice as many Soldiers attributed their musculoskeletal pain to wearing body armor than to job tasks and PT. In addition, there was a significant positive correlation between Soldiers who wore the body armor for four hours or more a day and self-reported musculoskeletal complaints. These results demonstrate a need to consider the potential adverse effects of individual body armor on combat Soldiers.