A mediated-reality system for surgical applications incorporates pre-operative images and real-time captured images of a surgical site into a visualization presented on a head-mounted display worn by a surgeon during a surgical procedure. The mediated-reality system tracks the surgeon's head position and generates real-time images of the surgical site from a virtual camera perspective corresponding to the surgeon's head position to mimic the natural viewpoint of the surgeon. The mediated-reality system furthermore aligns the pre-operative images with the real-time images from the virtual camera perspective and presents a mediated-reality visualization of the surgical site with the aligned pre-operative three-dimensional images or a selected portion thereof overlaid on the real-time images representing the virtual camera perspective.