The marked female predominance in cases of idiopathic chronic cough and its association with mild chronic lymphocytic airway inflammation suggests an underlying autoimmune process. We set out to test the hypothesis that idiopathic chronic cough is associated with other organ-specific autoimmune diseases in a case control study. Twenty-two patients with idiopathic chronic cough and 65 community-matched controls for age and sex who responded to a self-administered questionnaire were asked about the presence of autoimmune disease, other medical problems and drug history. All subjects were invited to have a blood test for an autoimmune screen. Thirteen out of 22 (59%) patients with idiopathic chronic cough and eight out of 65 (12%) age- and sex-matched controls reported organ-specific autoimmune disease (odds ratio 8.8; 95% confidence interval 2.4-31.8, P<0.001). Organ-specific autoantibodies were present in a significantly higher proportion of cases than controls (40% vs. 13%; P = 0.047). These findings suggest a relationship between idiopathic chronic cough and organ-specific autoimmunity.