Training of laparoscopic surgery in Virtual Reality (VR) environment has been proved as an effective step before clinical practice. Tracking the position of instruments in realtime is an essential part of developing a VR trainer. In this study, we used Microsoft Kinect and color markers instead of using similar traditional means such as mechanical sensors. The orientation and position of instruments were determined and compared with the results obtained using the SinaSim commercial laparoscopic surgery trainer, which measures these values using encoders. The final results indicated that even though the newly developed systems possess an inferior accuracy compared to the mechanical sensors, low cost and portability makes it capable of replacing traditional methods of tracking.