New display technologies enable the usage of 3D-visualization in a medical context. Even though user performance seems to be enhanced with respect to 2D thanks to the addition of recreated depth cues, human factors, and more particularly visual comfort and visual fatigue can still be a bridle to the widespread use of these systems. This study aimed at evaluating and comparing two different 3D visualization systems (a market stereoscopic display, and a state-of-the-art multi-view display) in terms of quality of experience (QoE), in the context of interactive medical visualization. An adapted methodology was designed in order to subjectively evaluate the experience of users. 14 medical doctors and 15 medical students took part in the experiment. After solving different tasks using the 3D reconstruction of a phantom object, they were asked to judge their quality of the experience, according to specific features. They were also asked to give their opinion about the influence of 3D-systems on their work conditions. Results suggest that medical doctors are opened to 3D-visualization techniques and are confident concerning their beneficial influence on their work. However, visual comfort and visual fatigue are still an issue of 3D-displays. Results obtained with the multi-view display suggest that the use of continuous horizontal parallax might be the future response to these current limitations.