Background Analysis of surgical instrument motion is applicable in surgical skill assessment and monitoring of the learning progress in laparoscopy. Current commercial instrument tracking technology (optical or electromagnetic) has specific limitations and is expensive. Therefore, in this study, we apply inexpensive, off-the-shelf inertial sensors to track laparoscopic instruments in a training scenario. Methods We calibrated two laparoscopic instruments to the inertial sensor and investigated its accuracy on a 3D-printed phantom. In a user study during a one-week laparoscopy training course with medical students and physicians, we then documented and compared the training effect in laparoscopic tasks on a commercially available laparoscopy trainer (Laparo Analytic, Laparo Medical Simulators, Wilcza, Poland) and the newly developed tracking setup. Results Eighteen participants (twelve medical students and six physicians) participated in the study. The student subgroup showed significantly poorer results for the count of swings (CS) and count of rotations (CR) at the beginning of the training compared to the physician subgroup (p = 0.012 and p = 0.042). After training, the student subgroup showed significant improvements in the rotatory angle sum, CS, and CR (p = 0.025, p = 0.004 and p = 0.024). After training, there were no significant differences between medical students and physicians. There was a strong correlation between the measured learning success (LS) from the data of our inertial measurement unit system (LSIMU) and the Laparo Analytic (LSLap) (Pearson’s r = 0.79). Conclusion In the current study, we observed a good and valid performance of inertial measurement units as a possible tool for instrument tracking and surgical skill assessment. Moreover, we conclude that the sensor can meaningfully examine the learning progress of medical students in an ex-vivo setting.