Helicopter pilots espouse ergonomically unfavourable postures and endure vibration which result in low back pain. The objective of this study was to investigate the effects of a helicopter flight on pilots back and shoulder muscles using surface Electromyography (sEMG) analysis. This study also correlates low back pain symptoms from Rehabilitation Bioengineering Group Pain Scale (RBGPS) questionnaire with muscle fatigue rates obtained. RBGPS was administered on 20 Coast Guard helicopter pilots. sEMG was acquired before and after flight from erector spinae and trapezius muscles in 8 of these 20 pilots. Statistical analysis of time and frequency domain parameters indicated significant fatigue in right trapezius muscle due to flying. Muscle fatigue correlated with average duration of flight (r2 = 0.913), total service as pilot (r2 = 0.825), pain (r2 = 0.463) and total flying hours (r2 = 0.507). However, muscle fatigue weakly correlated with Body Mass Index (BMI) (r2 = 0.000144) and age (r2 = 0.033). © 2011 Elsevier Ltd and The Ergonomics Society.