In our study, we introduce the use of a scrotal septal skin flaps in repair of hypospadias. Between June 2006 and October 2008, 30 patients were treated by using a penile local flap to reconstruct the urethra, and a scrotal septal skin flap to cover the wound located on the ventral side of the penis. Of 30 patients, 4 presented with urine leakage, but this condition healed spontaneously after 2 to 4 weeks. Urine leakage healed without problem in the remaining patients, and they had unobstructed urinary flow. Additionally, they all were satisfied with genital appearance after the reconstruction. We conclude that our method is a convenient means to cover the wound at the ventral side of the reconstructed urethra by using a scrotal septal skin flap during hypospadias repair. This procedure provides good urinary function and satisfactory appearance to the patients. In addition, this method solves the problem of very limited local tissue for urethral reconstruction in the hypospadias patient.