The aim of this paper is to present Cyprus’ initiative for the design and the implementation of the prototype of the integrated electronic health record at a national level that will establish the foundations of the country’s broader eHealth ecosystem. The latter, requires an interdisciplinary approach and scientific collaboration among various fields, including medicine, information and communication technologies, management, and finance, among others. The objective, is to design the system architecture, specify the requirements in terms of clinical content as well as the hardware infrastructure, but also implement European and national legislation with respect to privacy and security that govern sensitive medical data manipulation. The present study summarizes the outcomes of the 1st phase of this initiative, which comprises of the healthcare as well as the administrative requirements, user stories, data-flows and associated functionality. Moreover, leveraging the HL7 Fast Healthcare Interoperability Resources (FHIR) standard we highlight the concluded interoperability framework that allows genuine cross-system communication and defines third-party systems connectivity.