A three-dimensional vision system for guiding a surgical/diagnostic instrument in the body of a patient, comprising a plurality of vision devices (3) of the optical type that can be arranged in different positions around a shared area of surgical intervention (5) in which there is arranged a patient on whom the procedure is to be performed, in order to observe the patient (6) from different viewpoints. Each vision device (3) achieves a stereoscopic vision system suitable to identify first optical markers (17) carried by a patient marker (18) which is arranged in a stable and predetermined position on the body of the patient (6) and second optical markers (19) carried by an instrument marker (20) which is carried by an instrument (21) used to perform a diagnostic/surgical procedure on the patient. The overall coordinatesCg of the instrument marker (20) are calculated taking into account the information processed by the different vision devices (3) operating in parallel； the overall coordinates Cg are made available to a virtual navigation system suitable to represent a three-dimensional image of the body of the patient (6) on which a three-dimensional model of the instrument (21) is represented, positioned and orientated based on the overall coordinates Cg thus determined.
