With the ongoing development in the field of Medical Informatics, the availability of cross-references and the consistency of coverage between terminologies become critical requirements for clinical decision support. In this paper, we examine the possibility of developing a framework that highlights and exposes hierarchical incompatibilities between different medical terminologies in order to facilitate the process of achieving a sufficient level of consistency between terminologies. For the purpose of this research, we are working with the Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT) and the National Drug File - Reference Terminology (NDF-RT) – a clinical terminology focused on drugs. For discovery of inconsistencies we built an automated tool.