The invention includes a medical document handling system and method and automated coding systems and methods for assigning predetermined medical codes to medical documents based on the documents' contents. The invention functions by analyzing electronic medical records and extracting medical information using natural language processing and machine learning. The system collects and amalgamates medical documentation in various formats from multiple sources and locations, normalizes the information, analyzes the information, recognizes information indicating contents corresponding to classification codes, assigns classification codes, and presents information in context correlated to medical records for billing and other purposes.