The use of electronic health records for clinical research offers access to large-scale real-world data, but it requires the accurate transformation of data across clinical data repositories. In this study, we evaluate the data quality and completeness in three repositories (DWH, FHIR, and TriNetX) at Erlangen University Hospital. Key data elements (diagnosis, procedure, and laboratory codes) were analyzed, alongside a specific research question. Our results show good overall consistency, but discrepancies arise due to differences in code systems, data filtering, and the mapping process. These findings highlight the importance of critically assessing data provenance and the transformation processes when conducting multicenter research. Understanding the strengths and limitations of each repository is essential for ensuring high-quality research outcomes.