Abstract. Decision support systems based on computerized Clinical Protocols (CP) and Clinical Practice Guidelines (CPG) fall short when dealing with patient co-morbidites, as this demands the concurrent merging of multiple CP/CPG. We present an ontology-based approach for the merging of CPG and CP at two levels–i.e. knowledge modeling level and knowledge execution level. We have developed specialized ontological modeling constructs to facilitate merging of CPG and CP. We demonstrate the merging of multiple location-specific CP and disease-specific CPG.