A 52-year-old woman complained of persistent discharge from an umbilicus which she had for 18 years. Abdominal X-ray showed a stone-like shadow measuring 5 x 3 cm at the 5th lumbar spine. Cystoscopic examination revealed a hole at the dome of the bladder and a ureteral catheter was inserted approximately 3 cm through the hole. Computerized tomography scan and magnetic resonance imaging demonstrated a cyst communicating to the umbilicus and bladder. The preoperative diagnosis was a patient urachus associated with stone. Urachal cyst containing a stone was removed and partial cystectomy was performed. The stone was a mixture of magnesium ammonium phosphate and calcium phosphate. Pathological examination showed no evidence of malignancy. More than 210 cases of urachal cyst have been reported in Japan. About 10% of the cases were associated with stones.