Navigation and wayfinding are well-known issues that people face in their life every day. In many situations, and especially in the case of medical facilities, it is vital that users find the desired destination quickly and successfully. This is not only about comfort, but also about life and health safety. In this regard, the development of an effective navigation system becomes an extremely important mission for health care institutions. Therefore, the eye-tracking technology, which makes it feasible to look at the problem through visitor’s eyes, appears to be a pertinent tool for an objective assessment of the existing navigation, as well as finding ways to optimize it. This article considers present approaches to the analysis of navigation systems dealing with a large number of clients and describes our visual navigation study conducted in a health center. The first part of our study included the current navigation environment evaluation and the decision-making points detection, serving as a starting point for the implementation of a new, user-oriented navigation in the medical center. In the second part of the study the effectiveness of the applied system was confirmed. The results obtained show that navigation environment improvement can significantly reduce users’ time to reach the goal, as well as length of their route. Thus, we managed to apply the eye-tracking method to the improve user experience in a medical establishment.