This paper presents a process of building a prototype of an educational application for teaching anatomy with elements of physiology, with use of a Virtual Reality environment. Preparation of mesh models of individual human organs is described, along with further visualization techniques, which were used to ensure a proper level of a visual representation. Stages of user interface preparation are also described – both visual and functional aspects covered – with a detailed review of a visual programming process, which was used to obtain a logical structure of connections inside the VR environment. Process of preparation of dynamic graphical data-namely animation of the pulmonary alveoli – and integration it with the virtual environment is also presented. The final application can be used in a number of ways, including large-screen stereoscopic projection with on- screen graphical user interface and single-user immersive stereoscopic projection using a head-mounted device with an optical tracking system. Results of assessment of the application advantages and disadvantages at the current stage of development allowed to formulate several directions of further advancement.