The electronic storage of medical patient data is becoming a daily experience in most of the practices and hospitals worldwide. However, much of the available data is in free text form, a convenient way of expressing concepts and events but especially challenging if one wants to perform automatic searches, summarization or statistical analyses. Information Extraction can relieve some of these problems by offering a semantically informed interpretation and abstraction of the texts. MedInX, the Medical Information eXtraction system presented in this book is designed to process textual clinical discharge records in order to perform automatic and accurate mapping of free text reports onto a structured representation. MedInX components are based on Natural Language Processing principles, and provide several mechanisms to read, process and utilize external resources, such as terminologies and ontologies. MedInX current practical applications include automatic code assignment and an audit system capable of systematically analyze the content and completeness of the clinical reports.