Intellectual disability (ID) is a common paediatric problem. Investigation focused on determining the aetiology of ID is warranted because a specific diagnosis may assist in prognostication, recurrence risk counselling, and identification of therapeutic and educational interventions. Three groups of screening investigations can be justified on the basis of expert opinion, common sense and the small body of published evidence-based medicine. First, investigations where current evidence justifies routine use in the investigation of ID; second, investigations which should be considered in all children with ID, although there is insufficient current evidence to support routine use; and finally, investigations which currently have an unclear role in children with ID and should be restricted to specific clinical situations unless further evidence suggesting otherwise emerges. There is a great need for systematic evaluation of the diagnostic yield of investigation templates based on this proposed stratification of investigations.