A clinical information system (CIS) prototype was created from an Object-Oriented (OO) design. We experienced considerable difficulties when implementing the OO data model in a relational database management system (RDBMS), including lack of semantic power and support for complex objects, inability to encapsulate object methods, and performance degradation due to extensive join operations. This paper reflects on the experiences of a CIS research project and explores issues related to the use of RDBMS and Object-Oriented Database Management Systems (OODBMS) in CIS design and development.