Patient registries are an important instrument in medical research. Their implementation uses complex software systems to meet the wide spectrum of challenges. There is a wide range of systems available and a critical appraisal of their architecture is needed. Therefore, we developed, based on a systematic review of the literature, a checklist for patient registry software systems (CIPROS) which is organised in 67 items and 10 sections. CIPROS supports developers to assess requirements of an existing system. It also supports the reporting of patient registry software system descriptions in papers and it can be a first step to create standards for patient registry software systems.