Abstract: An integrated medical software system with embedded transcription functionality, and a method of using that system, is disclosed. The system includes a clinical software module that is configured to be executed by a processor to create an electronic document and to capture clinical data for a patient in the electronic document during an encounter with the patient. The system also includes a transcription software application that is configured to be executed by the processor to select predefined clinical data that will appear within the electronic document in response to speech commands and to automatically transcribe dictated clinical data that will appear within the electronic document in response to dictation, wherein the predefined clinical data being previously linked to at least one of a diagnosis code and a procedure code and the dictated clinical data being automatically linked to at least one of a diagnosis code and a procedure code as it is transcribed.