Background More than half a million refugees have arrived to Sweden during the last decade. The aim was to investigate differences between refugees and Swedish-born individuals regarding different specific somatic and mental disorders, and subsequent disability pension and mortality. Methods All refugees (n=239 742) and Swedish-born individuals (n=4 133 898), aged 19-60 years, resident in Sweden on 31st of December in 2009 were included in this population-based prospective cohort study. Data from six nationwide Swedish registers were linked by the unique anonymised identification number. HRs with 95% CIs were computed for disability pension and mortality 2010-2013 by Cox regression models. Results Compared with their Swedish-born counterparts with mental or somatic diagnoses, refugees with these diagnoses had a higher risk of subsequent disability pension and a lower risk of mortality. Highest estimates for disability pension were seen for refugees with neoplasm (HR: 1.72; 95% CI: 1.56 to 1.91), musculoskeletal disorders (HR: 1.57; 95% CI: 1.47 to 1.67), diseases of the circulatory system (HR: 1.33; 95% CI: 1.22 to 1.45), depressive disorders (HR: 1.31; 95% CI: 1.21 to 1.41) and diabetes mellitus (HR: 1.30; 95% CI: 1.15 to 1.47). The risk of mortality was lowest for refugees with regard to bipolar disorders (HR: 0.37; 95% CI: 0.16 to 0.82), post-traumatic stress disorder (HR: 0.37; 95% CI: 0.25 to 0.54) and least pronounced in regard to neoplasm (HR: 0.69; 95% CI: 0.61 to 0.77) compared with Swedish-born with similar disorders. Conclusion Refugees have a generally higher risk of disability pension compared with Swedish-born with specific somatic and mental disorders. Despite this, refugees with all specific disorders have lower risk estimates of mortality, probably due to a healthy selection. The higher risk of disability pension might therefore be due to other causes besides poor health.