Abstract: Nosocomial infections or hospital acquired infections are diseases that develop during an admission to hospital and are a consequence of treatment, procedures of treatment or work of hospital staff. These infections are dangerous because they are caused by bacteria that are developed and transmitted within the hospital, where they may reach a high level of resistance to antibiotics. The goal of this study is to identify such infections for a single patient or hospital units and to create a real time information system for analyzing the microbiological data and to control the infections. In order to attain this objective, we introduce a knowledge based system approach for microbiological investigation to select the most suitable antibiotic therapy. The knowledge base of the proposed system has been obtained from international standard guidelines for microbiological laboratory practice, from experts’ suggestions. Also we present the overall structure of the system and its implementation. This system will help medical practitioners and physicians to adopt appropriate methodology for controlling nosocomial infections.