Background: The language, format and length of typical national health survey questionnaires may make them inaccessible to many school-aged children with an intellectual disability. Materials and Methods: Using the standard delivery protocol, the WHO Health Behaviour in School-aged Children (HBSC) Questionnaire, currently in use in 43 countries, was administered to 46 children (11-17 years) with intellectual disabilities of varying severity who were attending two special (i.e. non-mainstream) schools. Two alternative administration procedures were subsequently piloted with a purposive subsample of 15 of these pupils. Results: Using the standard protocol, just over half of the children were able to "complete" the survey questionnaire, although a high proportion of their responses proved to be uncodable. Using modified procedures, both completion rates and codable response rates were markedly increased. Conclusions: With relatively easy-to-achieve (albeit time-consuming) procedural modifications, it is possible to collect data on a wide range of health-related issues from a pupil group otherwise at risk of exclusion from school-based national surveys. Confidentiality issues remain, however, as do concerns about accuracy of reporting in some areas, including perceived well-being.