Background: Studies have highlighted the incidence and prevalence of chronic pain, which is an epidemic problem in all career sectors, as well as estimated the economic loss that follows its pathology. Several studies have indicated a high incidence of chronic osteoarticular pain in military service members, particularly in flight personnel. To date, no studies have estimated the incidence of pain pathology in the Italian military population, despite the implications related to flight qualification. Methods: A survey was conducted on helicopter flight personnel undergoing periodic annual evaluation. Results: A statistically significantly higher incidence of pain pathology than that reported in the global civilian population was demonstrated. More than 80% of the interviewed population reported moderate-to-severe back pain (45% in the lumbar tract and 38% in the cervical tract). Further, it was found that most staff with chronic pain do not use drugs or other treatments for severe pain because of concerns that such treatment approaches may compromise flight qualifications. Discussion: The present study observed a high incidence of pain in Italian military flight personnel and examined the degree to which this problem is undertreated in these individuals. To address this problem, further in-depth and larger investigations that include therapeutic protocols to resolve such pain pathologies should be conducted. Such investigations could help to reduce pain experienced by flight personnel and enhance the productivity of the Italian military forces while considering the pharmacologic limitations related to the task. Conclusion: Chronic lumbar and neck pain is more common in military helicopter crews than in the civilian population. The true figure is frequently underestimated because of staff concerns regarding the potential influence of therapies on work activity.