Assessment of the quality of medical care plays an increasingly important role in the German healthcare system. Requirements for quality indicators include validity, reliability, responsiveness, interpretability and feasibility. Because of the high impact of guidelines, quality indicators that are recommended in such guidelines are of special relevance. We conducted a systematic review of all German S3 guidelines (actual as of November 30(th), 2013) to investigate the proportion of guidelines recommending quality indicators, which categories to classify quality indicators were used, and whether quality indicators in German S3 guidelines were developed following evidence-based methods. In 34 from 87 S3 guidelines (39%) a total of 394 quality indicators were defined. The vast majority of the recommended quality indicators focused on process quality. Outcome indicators were only recommended in 9 S3 guidelines (10%). None of the guidelines analysed reported the properties of the recommended quality indicators. Despite the increasing relevance of quality assessment for all stakeholders in the German healthcare system only approximately 40% of the S3 guidelines define indicators to measure the quality of care. Recommendations to assess outcome indicators are only provided in 10% of S3 guidelines. The process of the development and recommendation of quality indicators is heterogeneous and frequently not transparently reported. The current practice for the recommendation and validation of quality indicators in German S3 guidelines does not meet the requirements of evidence-based healthcare. © Georg Thieme Verlag KG Stuttgart · New York.