Effective medical and biomedical engineering education is an important problem. Traditional methods are difficult and costly. That is why Virtual Reality is often used for that purpose. Educational medical VR is a well-developed IT field, with many available hardware and software solutions. Current solutions are prepared without methodological approach. As a result, each VR system used for medical purposes is unique - there is no standardization, which leads to increased development time and costs. The paper presents an original methodology that can be used for building immersive virtual reality (VR) applications dedicated to training medical skills. The methodology is named “knowledge-oriented medical virtual reality” (KOMVR), as it uses basic knowledge-engineering tools during processes of planning, building and verification of interactive educational solutions. The paper shows successive stages of the methodology and the tools used for its execution. Effectiveness of the proposed methodology is illustrated with a simple example – a human body atlas. Major time reduction can be achieved while using the methodology - time reduction in the presented case was from 50 to 14 working days. The proposed innovative approach can increase effectiveness of preparation of educational VR solutions in medicine, but also in other branches of engineering.