The creation of common and coherent information space for providing the diagnostic and treatment process expands opportunities of its improvement and optimization based on the computer technologies. The article proves the general technological principles of formalization of clinical information that enable to provide not only the automating the formation of electronic medical notes, but minimizing mistakes when formulating the clinical diagnosis, development and creation of support software diagnostic decision-making, automating the processes of clinical management, didactic problems of increasing the professional level. Besides, the offered technology of formalization of clinical information allows solving the individual issues, associated with a coreference problem that opens an opportunity of integrating various data in the common information space.