Due to its unique composition, the reconstruction of scrotal skin defects is a major clinical challenge. This study was designed to evaluate the effects of scrotal reconstruction, using skin grafts and skin flaps, on spermatogenesis. In Group 1, the rats did not undergo surgery and were used as controls. In Group 2, after removal of all of the scrotal skin to expose the testicles, the defect was repaired using a skin flap from the right groin region. In Group 3, the reconstruction was achieved using skin grafts. All the rats were killed at 2 months postoperatively and evaluated. The mean wet weights of the testicles in the control group were significantly higher compared with that of the graft group. The mean height of the germinal epithelium was significantly greater in the control and flap groups compared with that of the graft group. The Johnsen score for spermatogenesis in the control group was higher than that in the graft group. The use of flaps resulted in testicular function that was comparable to that of the control group, whereas the use of grafts resulted in diminished testicular function. Therefore, we suggest that flaps may be the first choice for scrotal reconstruction.