Clinicians are faced with the difficulty of filtering large quantities of information and incorporating evidence to make safe and accurate diagnostic, therapeutic and management decisions. One solution to this difficulty is the development of evidence-based decision support tools designed to provide relevant and up-to-date evidence to clinicians. However, as investigations of medical decision making have found that hypothesis generation and clinical reasoning differ as a function of expertise, the gathering, interpretation and use of evidence against hypotheses depends on the prior knowledge of the clinician. The specific focus of the study is to understand how clinical evidence is gathered and evaluated during diagnostic reasoning. Verbal data during clinical interactions with physicians, residents and final year medical students were collected and transcribed. The dialogues were analyzed using three levels of coding: cognitive, epistemological and linguistic pragmatic perspectives. Results show that: (a) the ability to index and use adequate evidence by physicians, residents and students is a function of the early generation of accurate hypotheses: and (b) strategies for resolving inconsistent evidence differ as a function of medical expertise. The relationship between these findings and its application for the development of adequate knowledge-based systems for indexing and retrieval is discussed.