Background Musculoskeletal disorders (MSD) are common among soldiers and constitute the most common reason for discontinuing military service within different military populations worldwide. The aims of this study were to investigate the prevalence of musculoskeletal disorders in two cohorts, 10 years apart, in the Swedish Armed Forces, to explore differences between these cohorts and to determine associated factors with MSD. Method Comparative cross-sectional study. Participants were recruited from the Swedish Armed Forces, i.e. soldiers preparing for international missions in 2002 and 2012. A total of 961 soldiers, 7% women, participated in the study. Data were collected using the Musculoskeletal Screening Protocol (MSP), which includes questions regarding prevalence of MSD in ten anatomical locations (neck, upper back, low back, shoulders, elbow, hand, hip, knee, lower limb and foot). An additional five questions concern perceived self-rated health, i.e. how the respondent perceives their own physical body, mental health, social environment, physical environment and work ability. Results Over a ten-year period, both point prevalence and one-year prevalence of MSD in any body part increased significantly, with point prevalence increasing from 7.1 to 35.2% (p < 0.001) and one-year prevalence from 27.9 to 67.9% (p < 0.001). The knee was the most common anatomic location for MSD in both cohorts. Across each anatomical location (neck, upper back, low back, shoulders, elbow, hand, hip, knee, lower leg and foot), both point prevalence (p < 0.039) and one-year prevalence (p < 0.005) increased significantly from 2002 to 2012. Most soldiers reported good to excellent perceived health, i.e. self-perception of their physical body, mental health, physical and social environments, and work ability. The odds of reporting one-year prevalence of MSD in any body part was 5.28 times higher for soldiers in Cohort 2012, 1.91 times higher in age group 31–40 and 2.84 times higher in age group 41 and above. Conclusions The prevalence of MSD increased remarkably over a ten-year period among Swedish soldiers preparing for international missions. With increasing age as one risk factor, systematic monitoring of MSD throughout the soldiers’ careers and implementation of targeted primary-to-tertiary preventive programs are thus important.