BACKGROUND Greece is striving to limit its health expenditure to essential needs. General practice and the provision of Primary Health Care (PHC) mainly take place in rural settings, where approximately 200 Primary Health Care Centres (PHCCs) have been established. In order to determine how to optimize the effectiveness and efficiency of PHC services, it is important to first gain insights into the providers' perspectives. The aim of the study was to assess the perceptions of General Practitioners (GPs) and the directors of PHCCs regarding the effectiveness of available PHC services, and to elicit suggestions on how current services could be improved. METHODS This qualitative study was based on semi-structured interviews. The setting was 21 PHCCs in the Epirus and Crete regions of Greece. Twenty-nine physicians were interviewed on aspects of capacity, resources, performance and quality of PHC services. Discussions were digitally recorded and transcribed verbatim. The transcriptions were then analysed using thematic content analysis. RESULTS The main identified barriers to providing high-quality PHC services were: PHC service shortages in workforce and equipment; inadequate GP and paramedic training; the absence of position/job descriptions or duty statements for GPs and other PHC personnel; and limited public awareness about the role of GPs. Suggestions for remodelling the current PHC system included: the introduction of new technologies; GP empowerment; leadership reforms; and mechanisms for evaluating of the quality of services. Finally, areas of concern regarding future development and utilisation of private PHC infrastructure and services were highlighted. CONCLUSIONS The methodology of this study and the results regarding remodelling the current PHC system could be used to inform policy-making in Greece, particularly in the current period of severe economic crisis; they may also be of relevance to other European countries facing similar challenges in allocating resources and reforming PHC.