Medical ontologies are developed to solve problems such as the demand for reusing, sharing and transmitting data. The unambiguous communication of complex and detailed medical concepts is a crucial feature in current medical information systems. In these systems, several agents must interact in order to share their results and, thus, they must use a medical terminology with a clear and nonconfusing meaning. The paper presents the inclusion of an especially designed medical ontology in the HECASE2 multi-agent system. HECASE2 has been developed to help doctors in applying clinical guidelines to their patients in a semiautomatic fashion. In addition, it shows how intelligent agents may take profit from the modelled medical knowledge to coordinate their activities in the enactment of clinical guidelines. Keywords. Knowledge representation, Ontologies, Multi-agent systems, Clinical guidelines