Building a clinical decision support system (CDSS) capable to collect process and diagnose data from the patients automatically, based on information, symptoms and investigations is one of the current challenges for researchers and medical science. The purpose of the current study is to design a cloud-based CDSS to improve patient safety, quality of care and organizational efficiency. It presents the design of a cloud-based application system using a medical based approach, which covers different diseases to diagnosis, differentiated on most important pathologies. Using online questionnaires, traditional and new data will be collected from patients. After data input, the application will formulate a presumptive diagnosis and will direct patients to the correspondent department. A questionnaire will dynamically ask questions about the interface, and functionality improvements. Based on the answers, the functionality of the system and the user interface will be improved considering the real needs expressed by the end-users. The cloud-based CDSS, as a useful tool for patients, physicians and healthcare providers involves the computer support in the diagnosis of different pathologies and an accurate automatic differential diagnostic system.