BACKGROUND Certifications for quality management systems or disease-specific certifications have become increasingly popular in the German healthcare system. For chronic or rare diseases, however, patient safety and a patient-centred healthcare management have high priority. These aspects are often not adequately accounted for by the usual certification models. METHODS The BQS Institute for Quality and Patient Safety has developed a certification for the Deutsche Myasthenie Gesellschaft (DMG), a patients' self-help organisation. Standards for the certification were drafted by medical experts on the basis of guidelines and the scientific literature and were implemented into applicable criteria by the BQS Institute. Special emphasis was placed on translating patients' needs into the criteria catalogue. RESULTS The certificate "Integrierte Myasthenie-Zentren der DMG" [Integrated Myasthenia Centres of the DMG] is based on an all-day audit and includes a peer review. The active involvement of patients in the audit teams and in the certification board ensures that patient-relevant aspects are consistently taken into consideration besides medical criteria and quality management requirements. Notwithstanding the high medical quality in the two hospitals participating in the pilot phase, additional potential for improvement could be identified during the audits. DISCUSSION Certifications issued under the responsibility of patient organisations meet the need for specific quality improvement instruments for chronic and rare diseases. Acceptance of those certifications is enhanced by peer reviewing during the audits. From the patients' viewpoint all important aspects were incorporated into the certification concept.