Background. Functional gastrointestinal disorders (FGIDs) are common in the general population worldwide. However, there is paucity of large sale surveys for prevalence of FGID in the military personnel. Methods. It is a cross-sectional study, using Rome III criteria for the diagnosis of FGID among the Chinese Air Force (CAF) workers. Results. Of 4633 registered male subjects, there were 818 (16.4%) air crew and 4170 (83.6%) ground personnel. FGIDs were identified in 1088 (23.48%) of cases. It was more prevalent in the ground personnel than air crew (24.02% versus 20.33%; P = 0.022). Based on Rome III criteria, the commonest disease category was functional gastroduodenal disorder (37.4%), whereas functional nausea and vomiting disorder (FNV) was the most frequent overall diagnosis. Functional dyspepsia (FD) with irritable bowel syndrome (IBS) was the leading FGIDs' overlap (3.9%). Conclusion. FGIDs in CAF population are rather underestimated. This necessitates preventive strategies according to job characteristics.