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Background: Clinical registries facilitate medical research by providing 'real data'. In the past decade, an increasing number of disease registry systems (DRS) have been initiated in Iran. Here, we assessed the quality control (QC) of the data recorded in the DRS established by Shahid Beheshti University of Medical Sciences in Tehran, the capital city of Iran, in 2021. Methods: The present study was conducted in two consecutive qualitative and quantitative phases and employed a mixed-method design. A checklist containing 23 questions was developed based on a consensus reached following several panel group discussions, whose face content and construct validities were confirmed. Cronbach's alpha was calculated to verify the tool's internal consistency. Overall, the QC of 49 DRS was assessed in six dimensions, including completeness, timeliness, accessibility, validity, comparability, and interpretability. The seventy percent of the mean score was considered a cut-point for desirable domains. Results: The total content validity index (CVI) was obtained as 0.79, which is a reasonable level. Cronbach's alpha coefficients obtained showed acceptable internal consistency for all of the six QC domains. The data recorded in the registries included different aspects of diagnosis/treatment (81.6%) and treatment quality requirements outcomes (12.2%). According to the acceptable quality cut-point, out of 49 evaluated registries, 48(98%), 46(94%), 41(84%), and 38(77.5%), fulfilled desirable quality scores in terms of interpretability, accessibility, completeness, and comparability, however, 36(73.5%) and 32(65.3%) of registries obtained the quality requirement for timeliness and validity, respectively. Conclusion: The checklist developed here, containing customized questions to assess six QC domains of DRSs, provided a valid and reliable tool that could be considered as a proof-of-concept for future investigations. The clinical data available in the studied DRSs fulfilled desirable levels in terms of interpretability, accessibility, comparability, and completeness; however, timeliness and validity of these registries needed to be improved. [ABSTRACT FROM AUTHOR]