Information technology advances may help in conducting epidemiological studies using web-based surveys. Questionnaire-based headache diagnosis should be validated against the doctor’s diagnosis. This study aimed to develop and validate a web-based diagnostic questionnaire for migraine, probable migraine (PM), and tension-type headache (TTH). We constructed a seven-item questionnaire for diagnosing migraine, PM, and TTH. A web-based survey was conducted among adults aged 20–59 years; migraine, PM, and TTH were diagnosed based on the responses. Validation interview was performed via telephone by a neurologist within 1 month after the web-based interview. Finally, 256 participants completed both web-based survey and validation interview. Of them, 121 (47.3%), 65 (25.4%), 61 (23.8%), and 9 (3.5%) were diagnosed with migraine, PM, TTH, and unclassified headache (UH), respectively in the web-based survey, whereas 119 (46.5%), 60 (23.4%), 74 (28.9%), 2 (0.8%), and 1 (0.4%) were diagnosed with migraine, PM, TTH, UH, and primary stabbing headache, respectively in the validation interview. The best agreement was found in migraine (sensitivity: 92.6%; specificity: 94.8%; kappa coefficient: 0.875), followed by TTH (sensitivity: 78.4%; specificity: 98.4%; kappa coefficient: 0.809). PM showed the least agreement (sensitivity: 85.0%; specificity: 92.9%; kappa coefficient: 0.757). In conclusion, our questionnaire is valid in identifying these headache disorders.
