The present study demonstrates a new experimental model to compare the efficacy of end-to-end and end-to-end neurorrhaphy in free muscle flap neurotization. Forty animals were used, divided into four equal groups named A, B, C and D. The peripheral stump of the thoracodorsal nerve was stitched end-to-end in groups A and C and end-to-side in groups B and D to the long thoracic nerve. Free functional muscle transfer was simulated by putting vascular clamps to the thoracodorsal artery (FD SS8R, F: 15 to 20 g) and vein (FD SS6R, F: 10 to 15 g) for 60 minutes and transecting and then restitching the origin and insertion of the latissimus dorsi muscle. Electromyographic and histological studies were performed 150 days following completion of the experiment. The results could indicate the possibility that end-to-side neurorrhaphy might be used in free functional muscle transfer as an alternative to end-to-end neurorrhaphy. We believe that the proposed experimental model is useful for the comparative study between end-to-end and end-to-side neurorrhaphy in free muscle flap neurotization, as these are pure motor nerves and innervate synergistic muscles, are in close approximation, and have similar diameters.