The package EMPTY has been developed with the aim of providing a tool based on well assessed methodological principles which can support both the organisation and use of medical knowledge for diagnostic and educational purposes. EMPTY is domain-independent and results in two interactive programs: ASK guides the acquisition of medical knowledge and RUN supports medical decision-making and provides facilities for medical education. The knowledge bases developed on ASK have a standard formal structure: they include taxonomies, definitions and descriptions of diseases, clinical findings and investigations; production rules for activation and refinement of diagnostic hypotheses; frame-like profiles of diseases; and quantitative criteria for scoring the clinical evidence on the base of available data.