A system for computer-aided surgery and diagnosis in anatomical regions comprising rigid, non-deformable parts or tissues, the system comprising an intra-operative computer guidance assembly which in turn comprises: i) a free-moving camera that is meant to acquire intra-operative images and video of an operating field, articular joint or anatomical cavity; ii) a visual marker, referred to as the World Marker or WM, which is an object that can be rigidly attached to a surface, and that comprises at least one planar facet with a known pattern whose system of coordinates defines a global or world system of coordinates; iii) a touch-probe that is a tool or instrument comprising a handgrip and a tip, and that has at least one visual marker, referred to as Tool Marker or TM, comprising at least one planar facet with a known pattern that defines a local system of coordinates where a position of the tip P T is known; iv) a plurality of surgical execution instruments, where each surgical execution instrument has at least one visual marker, also referred to as Tool Marker or TM, comprising at least one planar facet with a known pattern that defines a local system of coordinates in which a position of relevant points and parts in the surgical execution instrument are known; and v) an image processing system, that may correspond to or may be part of a computer and/or any other computing device, the image processing system comprising a memory and being configured to receive as input images and video acquired by the camera of (i), as well as commands that may be entered by a button panel, keyboard, camera buttons, foot switch and/or any other input interface, and that outputs processing results and guidance information to a display; wherein, upon attachment of the WM of (ii) in an arbitrary location in the surface of the rigid anatomical part of interest, such that WM and anatomical part do not move one with respect to the other, the image processing system is configured to execute steps comprising: vi) perform 3D reconstruction of points in the surface of the rigid anatomical part by means of processing of images and video of the touch-probe of (iii) pin-pointing those points while keeping both WM and TM of the probe in a Field-of-View or FOV of the camera of (i); and vii) use the 3D reconstruction results of (vi) to perform measurements, make inferences, or overlay a surgical plan with the patient's anatomy, in which case a 3D registration method may be used for determining a transformation that maps local coordinates in a surgical plan into world coordinates in the WM attached to anatomy of interest; and viii) provide assisted execution of a clinical procedure by using the said surgical execution instruments of (iv) while keeping both WM and TMs of the instruments in the FOV of the camera of (i) such that the said surgical execution instruments can be located in world coordinates and real-time guidance can be provided by relating these locations with 3D reconstructions results of (vi) and/or overlaid surgical plan of (vii). i) a free-moving camera that is meant to acquire intra-operative images and video of an operating field, articular joint or anatomical cavity; ii) a visual marker, referred to as the World Marker or WM, which is an object that can be rigidly attached to a surface, and that comprises at least one planar facet with a known pattern whose system of coordinates defines a global or world system of coordinates; iii) a touch-probe that is a tool or instrument comprising a handgrip and a tip, and that has at least one visual marker, referred to as Tool Marker or TM, comprising at least one planar facet with a known pattern that defines a local system of coordinates where a position of the tip P T is known; iv) a plurality of surgical execution instruments, where each surgical execution instrument has at least one visual marker, also referred to as Tool Marker or TM, comprising at least one planar facet with a known pattern that defines a local system of coordinates in which a position of relevant points and parts in the surgical execution instrument are known; and v) an image processing system, that may correspond to or may be part of a computer and/or any other computing device, the image processing system comprising a memory and being configured to receive as input images and video acquired by the camera of (i), as well as commands that may be entered by a button panel, keyboard, camera buttons, foot switch and/or any other input interface, and that outputs processing results and guidance information to a display; vi) perform 3D reconstruction of points in the surface of the rigid anatomical part by means of processing of images and video of the touch-probe of (iii) pin-pointing those points while keeping both WM and TM of the probe in a Field-of-View or FOV of the camera of (i); and vii) use the 3D reconstruction results of (vi) to perform measurements, make inferences, or overlay a surgical plan with the patient's anatomy, in which case a 3D registration method may be used for determining a transformation that maps local coordinates in a surgical plan into world coordinates in the WM attached to anatomy of interest; and viii) provide assisted execution of a clinical procedure by using the said surgical execution instruments of (iv) while keeping both WM and TMs of the instruments in the FOV of the camera of (i) such that the said surgical execution instruments can be located in world coordinates and real-time guidance can be provided by relating these locations with 3D reconstructions results of (vi) and/or overlaid surgical plan of (vii).