New technologies involve in health domain as in every field of our entire life. This paper presents a study on the surgical instruments which are an indispensable part of health institutions. In the study, an application-based software approach is introduced to track the surgical instruments on which square barcodes were placed via laser printers. Either in the literature or in the industrial sense, the surgical instrument tracking systems are at the prototype stage. The result of the feasibility studies clearly indicates the major requirements of this industrial domain: Turkish and user-friendly interface, efficiency and dynamic surgical instrument tracking system. In order to answer these needs, in this paper, Surgical Instrument Tracking System (CATS), which performs the monitoring/tracking of surgical instruments in health institutions, is presented. In particular, the track of these tools is provided via optic barcode readers and user-friendly workstations that are placed in various units of the healthcare institution (especially in centralized sterilization unit). With this study, every phase of sterilization cycle can be controlled. The system also aims to prevent the loss (and theft) of surgical instruments and to determine missing/incomplete surgical containers more quickly and effectively.