The aim of this study was to determine the influence of stump rotation (fascicular cross-connection) on nerve autograft functional recovery. Thirty rat sciatic nerves were transected and repaired by autograft. The rats were divided into 3 groups according to the number of stump rotations of the autograft: (1) plain graft (PG-g, with no change in fascicular orientation, no difference in diameter), (2) graft rotation (GR-g, with no change in fascicular orientation, and diameter difference between fascicles), (3) stump rotation (SR-g, with cross-connection and diameter difference between fascicles). Relative gastrocnemius muscle weight and nerve fiber count were examined as anatomic recovery indices, and autotomy score (ATS) and toe-out angle as functional recovery indices. The results showed that SR-g had a significantly low functional recovery compared with PG-g and GR-g. However, there was no difference found in the anatomic recovery. These findings suggest that the stump rotation in nerve autograft had no effect on neural regeneration and muscle reinnervation; however, it had a negative effect on functional recovery. Because GR-g was similar to PG-g rather than SR-g in functional recovery, the diameter difference between fascicles appears to have had little effect on the functional recovery. The results of this study suggest that a novel approach to ATS interpretation is needed. It is recommended that (1) ATS 2 be considered the onset of autotomy instead of ATS 1; and (2) the frequency of "ATS 2 and above" should be considered for the comparison of the autotomy rather than the mean ATS.