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This study evaluated the effect of modified end-to-side neurorrhaphy on functional recovery by modulating the epineurial window and contact areas, with a donor nerve, using a rat median nerve and finger flexors. Grasping testing, muscle contractility testing, and a histological study were performed 20 weeks after surgery. The modified end-to-side repair can enhance axonal sprouting from an intact nerve, and improve the functional recovery. Either the epineurial window surface area, or the contact configuration with the donor nerve is an important factors in an end-to-side coaptation model.