This paper reports on the development of a smart sensor array consisting of selective gas sensing elements for use in disease diagnosis to monitor signaling gases. These are gases typically found in exhaled human breath that can serve as biomarkers for specific diseases. Utilizing the polymorphic selectivity of semiconducting metal oxides and by employing temperature modulation we have developed a smart gas selective sensor array able to identify and discriminate between isoprene, NOx, alcohols and amines/NH3. The sensing elements are thin films based on the various polymorphs of molybdenum trioxide. A breath analysis system based on our smart sensor array can be used for non-invasive monitoring and differential diagnosis of diseases.