Abstract The European Health Data Space (EHDS) promotes health data sharing and secondary use across Europe. The QUANTUM project focuses on labelling data quality (DQ), utility, and maturity to support EU-wide standards within this context. This study examines current DQ assessment practices in European Data Holder institutions to inform the design of a labelling tool for the EHDS. The study explored institutional practices for DQ assurance and assessment through a survey of EU-wide Data Holders and a literature search on open-source health DQ tools with potential for labelling. The survey targeted QUANTUM partners and external institutions, addressing DQ practices and tools. The literature review followed PRISMA guidelines and combined PubMed, AI-based queries, and known sources. We obtained survey responses from 27 Institutions across 13 European countries. The results showed a high variety and heterogeneity in DQ practices and tools used, including in-house developed tools, open-source tools, commercial products, and manual procedures. Most practices allowed customization of DQ dimensions and export of DQ analyses. The systematic review identified 66 DQ tools, 53% specific to data types such as electronic health records, omics or imaging, and 47% general-purpose. The diverse DQ institutional practices and tools emphasize the need for an interoperable self-assessment DQ labelling tool that guides the measurement and completion of consolidated metrics aligned with the EHDS regulations. Based on these findings, the QUANTUM project is developing this tool to support DQ labelling of Data Holders’ datasets candidate to publication at EU Health Data Access Bodies.