There are reports suggesting that people with Klinefelter’s syndrome may be at increase risk of some autoimmune diseases, but the evidence is not substantial. We wanted to add to the evidence by systematically assessing the risk of autoimmune diseases in a national cohort of people with KS. We selected records of all people with Klinefelter’s Syndrome in a record-linked dataset of all hospital day cases and inpatient admissions in England, 1999–2011; and then followed them up by electronic record linkage to identify the occurrence of autoimmune diseases. We compared their occurrence in the KS cohort with a control cohort, studied in the same way, and expressed the results as rate ratios. Of 30 autoimmune diseases studied in people with KS, there were significantly increased risks of seven–Addison’s disease, diabetes mellitus type 1, multiple sclerosis acquired hypothyroidism, rheumatoid arthritis, Sjogren’s syndrome and systemic lupus erythematous. We concluded that people with KS have increased risk of some autoimmune diseases, particularly those that are female predominant. The increased risk of autoimmune diseases associated with the XXY karyotype may hold clues to the pathogenesis of some aspects of autoimmunity.