The distinctive quality of the new social structure is that information becomes the only factor of production. In today's organizations, public administrators are directly responsible for applying information to administrative processes. In addition to his managerial responsibilities, a knowledge based organization requires every employee to take responsibility for achieving efficiency. This has increased the importance of information systems in the decision-making process. Information systems consist of computer and communication technology, data base management and model management and include activity processing system, management information system, decision support systems, senior management information system, expert systems and office automation systems. Information systems in the health sector aim at the management and provision of preventive and curative health services. The use of information systems in healthcare has the benefits of increasing service quality, shortening treatment processes, maximizing efficiency of the time, labour and medical devices. The use of information systems for clinical decision making and reducing medical errors in the healthcare industry dates back to the 1960s. Clinical information systems involve processing, storing and re-accessing information that supports patient care in a hospital. Clinical information systems are systems that are directly or indirectly related to patient care. These systems include electronic health/patient records, clinical decision support systems, nurse information systems, patient tracking systems, tele-medicine, case mix and smart card applications. Diagnosis-treatment systems are information-based systems used in the diagnosis and treatment of diseases. It consists of laboratory information systems, picture archiving and communication system, pharmacy information system, radiology information system, nuclear medicine information system. This study aims to evaluate the effectiveness of health information system applications in Turkey. The first part of the study focuses on the concept of information systems and the types of information systems in organization structures. In the second part, clinical information systems and applications for diagnosis-treatment systems in Turkey are examined. Finally, the study evaluates applications in the health sector qualitatively from the new organizational structure, which is formed by information systems.