A method for processing medical reports includes applying natural language processing methods to perform an initial segmentation of at least parts of textual contents of each medical report into information units, thereby identifying information units, such as text fragments, sentences or text passages, within the medical reports. The information units are classified into at least one context class to determine their appropriate context classes for a particular situation or application. The context classifications are created using a grammar, e.g., a context-free grammar, and can then be used for automatically assigning each information unit to an appropriate context meta-information. The medical report may be annotated by assigning the information units to context meta-information determined by the context class, and the context meta-information may be used by other applications, e.g., dedicated mechanisms for clinical data integration, how to efficiently handle the available information units within medical reports.