Background <p>Hospital morbidity data are used for hospital reimbursement in many countries and are also critical for epidemiological profiling and health planning, both of which depend on data quality. Exploring the clinical coders' perspective is crucial for implementing targeted interventions in this field.</p> Objective <p>To identify the main factors influencing the quality of health registries, the coding process and data quality, from the perspective of clinical coders in Portugal.</p> Methods <p>We conducted a nationwide online survey of clinical coders, informed by prior focus groups and a literature review, to assess their perspectives on the quality of health records, the clinical coding process, and coded data.</p> Results <p>A total of 162 responses were obtained. Respondents primarily used electronic health records, including discharge notes, clinical diaries, and surgical reports. Common problems in health records included "copy-paste" practices (67%) and the use of unspecified acronyms (52%). Incomplete records, inconsistent information, and the lack of support affected coding quality. Half agreed that a reduction in the number of coders contributed to delays. Financial incentives for quality, software availability, and frequent internal audits were identified as priority measures to improve data quality.</p> Conclusion <p>This study highlights the importance of clinical documentation for coding accuracy. Despite the use of electronic health records and the transition to ICD-10-CM/PCS, difficulties such as “copy-paste” practices and the use of unspecified acronyms persist. Continuous training, standardisation of documentation practices, and collaboration between clinical coders and other health professionals are essential to ensure coding accuracy. These problems and potential improvements may affect national policymaking and initiatives such as the European Health Data Space and international health prioritisation.</p>