After restitution of motor function the grasping test alone is insufficient to figure out any further differences of axonal nerve regeneration of the median nerve in rats. To avoid this problem we developed a standardized electrophysiologic method for testing median nerve regeneration. Threshold, latency, compound muscle action potentials (CMAP) and velocity of neuromuscular transduction were recorded in 54 rats 20 weeks post-operatively. Animals of group 1 served as control group, no transection of the median nerve was carried out. Animals of groups 2 and 3 underwent either primary nerve coaptation or autologous nerve grafting after transection of the median nerve. To ensure validity of the method additional correlation between all parameters was investigated. Reliable electrophysiological results were observed in all animals. As expected, group 1 animals showed lowest threshold and latency and highest CMAP levels. Transection of the median nerve and additional nerve repair leads to significant increase of threshold and latency as well as reduction of CMAP. Furthermore, animals of group 3 showed higher levels for threshold and latency and reduced CMAP levels compared with animals of group 2. The grasping test alone could not demonstrate these slight differences 20 weeks post-operatively. Additionally, we observed strong correlations between threshold, latency and CMAP using the Spearman correlation ranking. We describe the usage of motor neurography as a reproducible and valid tool which should be mandatory for detailed analysis of regeneration in the rat median nerve model.