Gastrointestinal problems are common during wars, and they have exerted significant adverse effects on the health of service members involved in warfare. The spectrum of digestive diseases has varied during wars of different eras. At the end of the 20th century, new frontiers of military medical research emerged due to the occurrence of high-tech wars such as the Gulf War and the Kosovo War, in which ground combat was no longer the primary method of field operations. The risk to the military personnel who face trauma has been greatly reduced, but disease and non-battle injuries (DNBIs) such as neuropsychological disorders and digestive diseases seemed to be increased. Data revealed that gastrointestinal symptoms such as constipation, diarrhea, dyspepsia, and noncardiac chest pain are common among military personnel during modern wars. In addition, a large number of deployed soldiers and veterans who participated in recent wars presented with chronic gastrointestinal complaints, which fulfilled with the Rome III criteria for functional gastrointestinal disorders (FGIDs). It was also noted that many veterans who returned from the Gulf War suffered not only from chronic digestive symptoms but also from neuropsychological dysfunction; however, they also showed symptoms of other systems. Presently, this broad range of unexplained symptoms is known as “Gulf War syndrome”. The mechanism that underlies Gulf War syndrome remains unclear, but many factors have been associated with this syndrome such as war trauma, stress, infections, immune dysfunction, radiological factors, anthrax vaccination and so on. Some have questioned if the diagnosis of FGIDs can be reached given the complexity of the military situation. As a result, further studies are needed to elucidate the pathogenesis of gastrointestinal disease among military personnel.