Rodent models are used extensively for studying nerve regeneration, but little is known about how sprouting and pruning influence peripheral nerve fiber counts and motor neuron pools. The purpose of this study was to identify fluctuations in nerve regeneration and neuronal survival over time. One hundred and forty-four Lewis rats were randomized to end-to-end repair or nerve grafting (1.5 cm graft) after sciatic nerve transection. Quantitative histomorphometry and retrograde labeling of motor neurons were performed at 1, 3, 6, 9, 12, and 24 months and supplemented by electron microscopy. Fiber counts and motor neuron counts increased between 1 and 3 months, followed by plateau. End-to-end repair resulted in persistently higher fiber counts compared to the grafting for all time points (P < 0.05). Percent neural tissue and myelin width increased with time while fibrin debris dissipated. In conclusion, these data detail the natural history of regeneration and demonstrate that overall fiber counts may remain stable despite pruning.