Background: It is recognised that back pain (BP) is a debilitating medical problem in the soldier community, which limits operational readiness as well as work ability. As such, identification of risk factors is a necessity for effective preventive actions, but also regarded as important from a safety perspective. The aim of this prospective cohort study was therefore to identify risk factors for back pain and BP limiting work ability in active duty marines within a 6 and 12-month period. Methods: Demographic characteristics, health-related factors and occupational exposure information, as gathered from questionnaires, as well as clinical test of movement control among 137 Swedish marines were regressed with multivariable logistic regressions, and strength of associations was presented as odds ratio (OR) with 95 % confidence intervals (CI). BP within 6 and 12 months were used as primary outcomes, whereas BP limiting work ability within 6 and 12 months served as secondary outcomes. Results: Previous BP and tall body height (≥1.86 m) emerged as risk factors for back pain within 6 months (OR 2.99, 95 % CI 1.22-7.30; OR 2.81, 95 % CI 1.16- 6.84, respectively), and 12 months (OR 6.75, 95 % CI 2.30-19.80; 2.75, 95 % CI 1.21-6.29, respectively). Previous BP was also identified as risk factor for BP limiting work ability within 12 months (OR 6.64, 95 % CI 1.78-24.78), and tall body height emerged as a risk within both six (OR 4.30, 95 % CI 1.31-14.13) and 12 months (OR 4.55, 95 % CI 1.53-13.57) from baseline. Conclusions: Marines with a history of BP are at risk of further BP episodes, which, thus, emphasise the importance of early BP preventive actions. Tall body height also emerged as an important risk which may reflect that personal equipment and work tasks are not adapted for the tallest marines. While this should be considered when introducing new work equipment, further studies are warranted to clarify the underlying mechanism of this association.