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Strongly increased risks of all-cause and diagnosis-specific disability pension were observed among both women and men who were sickness absent due to musculoskeletal diagnoses, after adjustment for several potential confounders, including morbidity.Musculoskeletal disorders constitute major public health problems. Few studies have, however, examined risk of disability pension among persons sickness absent due to musculoskeletal diagnoses. Thus, we constructed a prospective nationwide population–based cohort study based on Swedish registers, consisting of all 4,687,756 individuals living in Sweden December 31, 2004/2005, aged 20–64 years, who were not on disability or old-age pension. Those individuals who were sickness absent in 2005 due to musculoskeletal diagnoses were compared to those sickness absent due to non-musculoskeletal diagnoses and those with no sickness absence. Musculoskeletal diagnoses were categorized as follows: 1) artropathies/systemic connective tissue disorders, 2) dorsopathies, and 3) soft tissue disorders/osteopathies/chondropathies/other musculoskeletal disorders. All-cause and diagnosis-specific incident disability pension were followed from 2006 to 2009. Incidence rate ratios (IRRs) and 95% confidence intervals (CIs) were estimated by Cox proportional hazards regression. In models adjusted for socio-demographic factors and morbidity, sickness absence due to all categories of musculoskeletal diagnoses was associated with 12- to 18-fold increased risks of all-cause disability pension (adjusted model, category 2 diagnoses, IRR = 18.57, 95% CI = 18.18–18.97). Similar associations were observed among both women and men sickness absent due to all 3 musculoskeletal diagnostic categories. Moreover, increased risks of disability pension because of cancer, mental, circulatory and musculoskeletal diagnoses were observed among individuals sickness absent because of any musculoskeletal diagnostic category (disability pension due to musculoskeletal diagnoses, adjusted model, category 2 diagnoses, IRR = 50.66, 95% CI = 49.06–52.32). In conclusion, this nationwide cohort study reveals strongly increased risks of all-cause and diagnosis-specific disability pension among those sickness absent due to musculoskeletal diagnoses.