This paper presents common issues associated with information retrieval from electronic medical records and presents linguistic approaches to resolve these issues. Linguistic analyses of three medical topics (heart attacks, smoking, and death reports) are presented to highlight common is- sues and our approaches to resolve them. We demonstrate how the Clinical Practice Analysis (CPA) system developed by Synthesys Technologies, Inc. enables the medical researcher to create powerful queries to retrieve in- formation about individual patients or entire patient populations quickly and easily. The efficiency of this system has been enhanced by the imple- mentation of linguistic generalizations specific to medical records, such as lexical variation, ambiguity, argument alternation, anaphora resolution, be- lief contexts, downward-entailing contexts and presupposition.