The present article analyses the development and implementation of quality management systems at institutes for clinical and theoretical research as exemplified by the Charité University Medical Centre's Institute for Social Medicine, Epidemiology, and Health Economics in Berlin. The Institute established its quality management system independently (i.e. without external consultants) and was able to fulfil the standard requirements within one year. The quality management system was successfully certified under European Standard DIN EN ISO 9001:2000 by an authorized external DIN-accredited inspection authority in October 2005 and recertified one year later. The certification covered the areas of research, teaching, and supporting administration. Our description of the individual steps involved and the corresponding timeline may be useful to organizations of a similar type and size seeking professional external certification.