Coded data are the basis of information systems in all countries that rely on Diagnosis Related Groups in order to reimburse/finance hospitals, including both administrative and clinical data. To identify the problems and barriers that affect the quality of the coded data is paramount to improve data quality as well as to enhance its usability and outcomes. This study aims to explore problems and possible solutions associated with the clinical coding process. Problems were identified according to the perspective of ten medical coders, as the result of four focus groups sessions. This convenience sample was sourced from four public hospitals in Portugal. Questions relating to problems with the coding process were developed from the literature and authors' expertise. Focus groups sessions were taped, transcribed and analyzed to elicit themes. Variability in the documents used for coding, illegibility of hand writing when coding on paper, increase of errors due to an extra actor in the coding process when transcribed from paper, difficulties in the diagnoses' coding, coding delay and unavailability of resources and tools designed to help coders, were some of the problems identified. Some problems were identified and solutions such as the standardization of the documents used for coding an episode, the adoption of the electronic coding, the development of tools to help coding and audits, and the recognition of the importance of coding by the management were described as relevant factors for the improvement of the quality of data.