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Abstract Background Initiatives such as “Choosing Wisely” in the USA and “Smarter Medicine” in Switzerland have published lists of widely overused health care services. The German initiative “Choosing Wisely Together (Gemeinsam Klug Entscheiden)” follows this example. The goal of our study was to prioritize important recommendations against the overuse and underuse of health care services. The final list of recommendations will be published in the German guideline “Protection against the overuse and underuse of health care”. Methods First, a multidisciplinary expert panel established a catalogue of prioritization criteria. Second, we extracted all the recommendations from evidence- and consensus-based German College of General Practice and Family Medicine (DEGAM) guidelines and National Health Care Guidelines (NVL). Third, the recommendations were rated by two independent panels (general practitioners and other health care professionals involved/not involved in guideline development). The prioritization process was finalized in a consensus conference held by DEGAM’s Standing Guideline Committee (SLK). Results Eleven prioritization criteria were established. A total of 782 recommendations were extracted and rated by 98 physicians and other health care professionals in a survey. In the voting process, more than 80% of the recommendations were eliminated. After the final consensus conference, twelve recommendations from DEGAM guidelines, nine DEGAM addenda and 17 NVL recommendations were chosen for inclusion in the guideline, for a total of 38 recommendations. Conclusion The selection procedure proved helpful in identifying the highest priority recommendations with which to combat the overuse and underuse of health care services. To date, in Germany there has been no attempt to compile such a list by using a systematic and transparent methodology. Hence, the guideline that results from this process can fill an important gap.