Atopic dermatitis (AD) is a common chronic skin disorder and well-known to be associated with other atopic conditions. There is increasing evidence for an association also with non-atopic conditions, including autoimmune diseases, but data are limited about several autoimmune diagnoses.To investigate the association between AD and autoimmune diseases.This case-control study used Swedish national health care registers. The source population comprised the entire Swedish population, 15 years or older, from 1968 through 2016. Cases, including all those with an inpatient diagnosis of AD (from 1968) and/or a specialist outpatient diagnosis of AD (from 2001), were matched by sex and age to healthy controls (104,832 AD cases, 1,022,435 controls).AD was significantly associated with one or more autoimmune diseases compared with controls (adjusted odds ratio (aOR) 1.97, 95% confidence interval (CI) 1.93-2.01), and this association was significantly stronger in the presence of multiple autoimmune diseases compared with only one. The association was strongest for autoimmune disorders involving the skin (aOR 3.10, 95% CI 3.02-3.18), the gastrointestinal tract (aOR 1.75, 95% CI 1.69-1.82), or the connective tissue (aOR 1.50, 95% CI 1.42-1.58). In the overall analysis, men with AD had a stronger association with rheumatoid arthritis and coeliac disease than women with AD. In sub-analyses, the findings remained stable in multivariable analyses after adjustment for smoking and parental autoimmune disease.This large population-based study indicates a significant autoimmune comorbidity of adults with AD, especially between AD and autoimmune dermatologic, gastrointestinal and rheumatologic diseases. Having multiple autoimmune diseases had a stronger association with AD than having only one autoimmune disease.