While employing the Holmium YAG laser, photonic technologies can help detect urinary stones and enhance safety for the patient. Our research group recently found that continuous monitoring of the fluorescence spectra of urinary calculi suffices to distinguish between stone, tissue, and endoscope components precisely and in real time. We hereby introduce our new automatic target identification system and the results of experimental studies we conducted. In this study, we review the research on in vitro and in vivo experiments we conducted developing and characterizing a novel target system, and summarize the key features of this new technology. This new system using intraoperative autofluorescence monitoring, enables the detection of the laser's target by analyzing the fluorescent spectra reflected from the target. The energy pulses are only emitted when a urinary stone is within reach of the laser fiber tip. Our experiments revealed that this autofluorescence-based automatic target recognition lithotripsy system delivers valuable diagnostic information to the surgeon in real time. Our system recognizes potential target structures via implemented fluorescence detection. After setting a fluorescence intensity threshold level, a feedback mode was employed that autonomously controls the Ho:YAG laser. During this procedure, the pulse emissions were controlled only by our system, not by the surgeon. The safety and effectiveness of this system has been successfully proven in animal studies. This new target system with a feedback mechanism provides certainty that even in the event of unintentional laser activation, the laser emission is blocked, thus preventing tissue damage and unnecessary heat generation. Ours is a promising approach with the potential to be used in various future urological and non-urological applications primarily to enhance patients' safety.