Chinese Medicine (CM) has been recognized as the popular complementary medicine in the world and the abundance of healing knowledge has been transmitted and enriched from generation to generation. The well-recorded archive of Chinese medical knowledge has grown and developed into very detailed theory and philosophy together with a comprehensive and subtle system of diagnosis. Recently, the Internet has been quite often used in a variety of applications for medical purpose, i.e. to provide real-time and platform-independent access which can 'build and share knowledge about clinical diagnosis experiences, knacks, diseases treatments, and even prescriptions. In this respect, there is a real need of an intelligent system for Chinese medical physician or education because Chinese medicine has evolved complex methods of diagnosis and treatment tailored to the individual's subtle patterns of disharmony. This allows it not only to treat fully manifest diseases, but also to assist in maintaining health and balance to prevent illnesses from occurring. Ontologies become an important mechanism to build knowledge-based systems. The role of ontologies is to capture domain knowledge and provide a commonly agreed upon understanding of a domain. The advantages include the sharing and re-use of knowledge, and the better engineering of knowledge-based system with respect to acquisition, verification, and maintenance. In this paper, we propose a unifying framework for intelligent disease diagnosis system named CMDS - Chinese Medical Diagnostic System where the medical ontology has been integrated for the system development, and the methodologies of its implementation for digestive health. CMDS uses web interface and expert system technology to act as human expertise and diagnose a number of digestive system diseases. Besides, to efficiently elicit the knowledge of digestive system from domain experts and construct the medical ontology, a hybrid knowledge acquisition strategy is proposed. CMDS provides a truly precise analysis for digestive system disease and the prototype system can diagnose up to 50 types of diseases amongst 10 species of primary digestive system, and just uses over 500 rules and 600 images for various diseases. The satisfactory performance of the system has proven that it could serve the educational purpose, act as a consultant role and the functionality can be extended to the whole body health system. (C) 2006 Elsevier Ltd. All rights reserved.