Aim: Recently, attention has focused on the health inequalities experienced by people with intellectual disabilities (ID) when compared with the general population. To inform policies aimed at equalizing health opportunities, comparable evidence is needed about the aspects of their health that may be amenable to intervention. Method: Applying the framework of the European Community Health Indicators (ECHI) for the general population, the Pomona group developed a set of health indicators reflecting aspects of the health of people with ID: socio-demographic data, health status, health determinants and health systems. Results: This paper documents the procedures that partners carried out in 13 European countries. The process comprised a search for evidence in published literature; consultation with advocates, family members and health professionals; and analyses of national and international databases. Indicators were selected if they were appraised as important, useful, measurable and if resulting data would enable comparisons between the health of people with ID and that of the general population. Conclusion: The thus developed indicator set that is aligned with ECHI will permit investigators to compare key aspects of health of people with ID with those of people in the general population within Europe. The final set of 18 indicators will be applied in the Pomona 2 project (2005-08) to gather information about the health of samples of adults in 14 participating European countries.