Few well-constructed studies have systematically evaluated medical investigation protocols for children with autistic spectrum disorders. This is in large part due to the heterogeneous nature of the population and changing diagnostic frameworks. This review outlines the studies that have directed investigation strategies to date, and discusses how these might be applied in the clinical situation. The importance of listing the conditions that may be present on the basis of the specific clinical presentation, and using a thorough history and examination to generate a pre-test probability of the target disorders is emphasized if tests are to be useful in directing therapy or broader management approaches.