A 31-year-old male with true hermaphroditism and a 46, XX karyotype who underwent gonadectomy and extirpation of the internal sex organs at the age of 4 had a large stone 4 cm in diameter in the residual male vagina. He complained of pain on micturition, hematuria, and rectal pressure. Urethroscopy and retrograde urethrography disclosed an ostium of the male vagina in the prostatic urethra, and an impacted intravaginal stone. Transurethral electrohydraulic lithotripsy was performed. Extracorporeal shock wave lithotripsy and transurethral lithotripsy were performed for the residual stones. All stones and fragments were spontaneously passed. The stone was composed of calcium phosphate and ammonium acid urate.