Aims: To investigate the longitudinal relation between physical capacity (isokinetic lifting strength, static endurance of the back, neck, and shoulder muscles, and mobility of the spine) and low back, neck, and shoulder pain. Methods: In this prospective cohort study, 1789 Dutch workers participated. At baseline, isokinetic lifting strength, static endurance of the back, neck, and shoulder muscles, and mobility of the spine were measured in the pain free workers, as well as potential confounders, including physical workload. Low back, neck, and shoulder pain were self-reported annually at baseline and three times during follow up. Results: After adjustment for confounders, Poisson generalised estimation equations showed an increased risk of low back pain among workers in the lowest sex specific fertile of performance in the static back endurance tests compared to workers in the reference category (RR = 1.42; 95% CI 1.19 to 1.71), but this was not found for isokinetic trunk lifting strength or mobility of the spine. An increased risk of neck pain was shown for workers with low performance in tests of isokinetic neck/shoulder lifting strength (RR = 1.31; 95% CI 1.03 to 1.67) and static neck endurance (RR = 1.22; 95% CI 1.00 to 1.49). Among workers in the lowest fertiles of isokinetic neck/shoulder lifting strength or endurance of the shoulder muscles, no increased risk of shoulder pain was found. Conclusions: The findings of this study suggest that low back or neck endurance were independent predictors of low back or neck pain, respectively, and that low lifting neck/shoulder strength was an independent predictor of neck pain. No association was found between lifting trunk strength, or mobility of the spine and the risk of low back pain, nor between lifting neck/shoulder strength or endurance of the shoulder muscles and the risk of shoulder pain.