A system for dynamic augmented reality imaging of an anatomical site includes at least one image capturing device for capturing first real-time images of the site, at least one display device for displaying first images captured by the device, storage means for storing at least one second anatomical image of the site and an electronic device having a controller configured to receive and process the images. The controller is configured to display an augmented reality image obtained by superimposing images on the first image by identifying common reference elements of the images, and the common reference elements are identified automatically or manually. The second image is in 3D made up of portions of fan or cone beam computed tomography or magnetic resonance images depicting internal structures of the site. The augmented reality image is clipped to the site by the elements, irrespective of the spatial position of the electronic device.