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Obesity is associated with musculoskeletal pain and osteoarthritis. This study compares the prevalence of work-restricting musculoskeletal pain in an obese and a general population and investigates changes in the incidence of and recovery from musculoskeletal pain after bariatric surgery or conventional obesity treatment. A random sample of 1135 subjects from a general population was compared with 6328 obese subjects in the Swedish obese subjects (SOS) study. For the obese subjects, information about musculoskeletal pain was also collected 2 and 6 years after obesity surgery or the start of non-surgical treatment. In both sexes, self-reported work-restricting pain in the neck and back area and in the hip, knee and ankle joints was more common in the obese subjects than in the general population (odds ratios (ORs) ranging from 1.7 to 9.9, P<0.001). Operated obese women had a lower incidence of work-restricting pain in the knee and ankle joints compared with the conventionally treated control group over 2 and 6 years (ORs 0.51–0.71). Among subjects reporting symptoms at baseline, the recovery rate for pain in the knee and ankle joints in men and pain in the neck and back and in the hip, knee and ankle joints in women improved in the surgical group compared with the control group after 2 years (ORs 1.4–4.8). Obese subjects have more problems with work-restricting musculoskeletal pain than the general population. Surgical obesity treatment reduces the long-term risk of developing work-restricting musculoskeletal pain and increases the likelihood of recovering from such pain.