Navigation, tracking and guiding system (1) for the positioning of operatory instruments (5) inside the body of a patient (P) comprising a control unit (2), a display (3) and first detecting means (4) for determining the spatial position of the viewer (3). The system (1) further comprises a sensor associated to an operatory instrument (5) and insertable inside the internal portion (Pi) of the body of the patient (P). The probe comprises at least one optical guide, having dispersion zones of a luminous flux generated inside the optical guide and detecting means for the detection of the dispersion of the luminous flux, in order to identify the spatial arrangement of the probe when inserted within the patient (P). The control unit (2) is configured to project on the viewer (3) an image of the internal state of at least one internal portion (Pi) of the body of the patient (P) and the image of the probe based on the identified spatial arrangement.