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End-to-side (ETS) neurorrhaphy was a useful tool in peripheral nerve repair and “baby-sitter” procedure. The study was designed to evaluate the long-term efficacy of ETS with epineurial window and 40% partial donor neurectomy in rats.A total of 60 Lewis rats were divided into three groups (n = 20, each group): following peroneal nerve transection, rats in Group A underwent end-to-end neurorrhaphy; rats in Group B underwent ETS neurorrhaphy of the distal peroneal nerve stump to an epineurial window on the tibial nerve; and rats in Group C underwent ETS neurorrhaphy of the distal peroneal nerve stump to the tibial nerve with 40% partial neurectomy. At 6, 12, 18, and 24 weeks after surgery, electrophysiology, muscle tension, myelinated fiber regeneration, cross-sectional area of muscular fiber, and muscle weight were analyzed.Histology exhibited apparently increased number and size of myelinated fibers in peroneal nerves in Group C, compared with those in Group B. More superior recovery was demonstrated in the electrophysiology and axon regeneration of the peroneal nerves, as well as the maintenance of muscle force, wet weight, and fiber size of the anterior tibial muscles in Group C than those in Group B.ETS neurorrhaphy with partial donor neurectomy can achieve higher efficacy in functional and structural recovery of the recipient system. This study provides the evidence of long-term follow-up for the further investigation of ETS neurorrhaphies with different modalities in peripheral nerve repair and in “baby-sitter” procedure.