OBJECTIVES: Injury surveillance is imperative for injury prevention but difficult in military populations. Our objective was to accurately describe the pattern of musculoskeletal complaints among Royal Australian Air Force (RAAF) fast jet aircrew (FJA) using the validated University of Canberra Fast Jet Aircrew Musculoskeletal Questionnaire (UC-FJAMQ) over a 2-year period, and determine injury burden on the workforce and operational capability. METHODS: 306 RAAF FJA were monitored over a 2-year period (4×5 month reporting periods). Musculoskeletal complaint episodes (MCEs) were captured weekly using the UC-FJAMQ. Time loss episodes (TLEs) were captured from the UC-FJAMQ and injury registers completed by embedded physiotherapists. Cumulative severity and operational impact scores from the UC-FJAMQ, and time loss duration, were used to describe severity and calculate burden. RESULTS: Mean weekly UC-FJAMQ response rate was 62%. 1012 MCEs were captured, with a mean weekly prevalence of 14.9% (95% CI 14.2-15.6), and incidence of 4.1 episodes per person-year (95% CI 3.9-4.4). A total of 145 TLEs were captured, with a mean 5-month prevalence of 12.4% (range 8.9-15.3%), and incidence of 0.37 episodes per person-year (95% CI 0.31-0.43). Spinal regions accounted for 81% of MCEs and contributed 76% and 85% of burden in relation to cumulative severity and operational impact, respectively. 57% of TLE burden came from spinal regions. CONCLUSIONS: Despite modest weekly UC-FJAMQ response rates, musculoskeletal complaints were shown to be widespread and negatively impact operational capability. Future injury prevention efforts among FJA should focus on spinal regions, particularly the neck.