In order to evaluate the impact of physical work exposure on differences in musculoskeletal symptom reported among Swedish farmers and referents, a cross-sectional, population-based cohort study was performed. Male farmers (N = 1221) and matched non-farmers (N = 1130) were invited to take part a survey in which 76 % participated. The analyses were based on 657 matched pairs. Lifetime incidence of musculoskeletal symptoms, information on work exposure, physical workload and leisure time physical activity were assessed by questionnaire and structured interview. Physical work capacity and muscle strength were measured. Farmers reported more low back and hip problems than the referents. After adjustment for the influence of work exposure factors, farmers still had a significant excess rate of low back and hip symptoms compared to the referents, and a significantly lower rate of neck and shoulder problems. In conclusion, work exposure explained some but not all of the farmer-referent differences in musculoskeletal symptom rates.