One of the most important problems about medical expert systems is that it is difficult for them to diagnose complicated cases. There are various approaches to overcome this problem, such as deeper knowledge representation, case-based reasoning. However, they are not sufficient to solve this problem completely. In order to solve this problem, we propose three-level hierarchical ontologies. For bridging between ontologles, qualitative dynsmics of disease’s progression (QUAD) and augmented automata model (ACAM) are introduced. We are developing a system, RS-QUAD (Reasoning System based on QUAlitative Dynamics of disease’s progression), which implements these two methods. This approach enables us to describe temporal progression of disease mechanisms end make it easier to interpret clinlca] manifestations and results of laboratory examination.