Assessment of minimally invasive surgical skills is a non-trivial task, usually requiring the presence and time of expert observers, including subjectivity and requiring special and expensive equipment and software. This study develops an algorithm for tracking laparoscopy instruments in the video cues of a standard laparoscopy training box with a single webcam camera and proposes new criteria to assess skill level using the extracted tool trajectories. Instrument tracking and assessment criteria together constitute a significant step towards developing a low cost, automated, and widely applicable laparoscopy training and assessment system using a standard physical training box equipped with a webcam. The developed visual tracking algorithm recovers the 3D positions of the laparoscopic instruments tips to which simple colored tapes (markers) are attached. The new assessment criteria are based on frequency analysis and linear discriminant analysis of the 3D reconstructed trajectories of the instruments. The performance of these proposed criteria are compared to the conventional criteria for laparoscopy training and demonstrated to be superior on the data we have recorded from six professional laparoscopy surgeons and ten novice subjects.