The aim of the present study was make chronic cough guidelines more practical and user friendly by developing an internet-based interactive diagnostic questionnaire for chronic cough. A prospective cohort study of chronic cough sufferers was conducted in the UK, following European Respiratory Society guidelines for the diagnosis and management of chronic cough. Depending on the response to 16 specific questions, the medical condition responsible for the patient's chronic cough was ascertained according to a predetermined diagnostic algorithm designed to differentiate the three common causes of chronic cough. Appropriate advice and treatment recommendations were then provided. 8,546 adults with chronic cough completed the Cough Clinic diagnostic questionnaire. 46.1% were suggested to have reflux, 38.7% asthma and 15.2% rhinitis. Participants found the website easy to use (94%), the advice helpful (73%) and that it helped them to communicate with their general practitioner better (60%), and 62% reported taking the recommended treatment. The Cough Clinic, an internet-based diagnostic site for chronic cough, had a large uptake by chronic cough sufferers in the UK. Almost half were diagnosed as having reflux as the probable cause of their chronic cough. Internet diagnosis by expert algorithm provides a novel mechanism for patients to access guideline-recommended therapies and enhances dialogue between patients and physicians.