Some autoimmune disorders have been linked to venous thromboembolism. We examined whether there is an association between autoimmune disorders and risk of pulmonary embolism. We followed up all individuals in Sweden without previous hospital admission for venous thromboembolism and with a primary or secondary diagnosis of an autoimmune disorder between Jan 1, 1964, and Dec 31, 2008, for hospital admission for pulmonary embolism. We obtained data from the MigMed2 database, which has individual-level information about all registered residents of Sweden. The reference population was the total population of Sweden. We calculated standardised incidence ratios (SIRs) for pulmonary embolism, adjusted for individual variables, including age and sex. 535,538 individuals were admitted to hospital because of an autoimmune disorder. Overall risk of pulmonary embolism during the first year after admission for an autoimmune disorder was 6·38 (95% CI 6·19-6·57). All the 33 autoimmune disorders were associated with a significantly increased risk of pulmonary embolism during the first year after admission. However, some had a particularly high risk--eg, immune thrombocytopenic purpura (10·79, 95% CI 7·98-14·28), polyarteritis nodosa (13·26, 9·33-18·29), polymyositis or dermatomyositis (16·44, 11·57-22·69), and systemic lupus erythematosus (10·23, 8·31-12·45). Overall risk decreased over time, from 1·53 (1·48-1·57) at 1-5 years, to 1·15 (1·11-1·20) at 5-10 years, and 1·04 (1·00-1·07) at 10 years and later. The risk was increased for both sexes and all age groups. Autoimmune disorders are associated with a high risk of pulmonary embolism in the first year after hospital admission. Our findings suggest that these disorders in general should be regarded as hypercoagulable disorders. Swedish Research Council, Swedish Council for Working Life and Social Research, Swedish Research Council Formas, Region Skåne. Copyright © 2012 Elsevier Ltd. All rights reserved.