We report a rare case of familial urachal disease associated with a congenital malformation. A 34-year-old woman was referred to our hospital with recurrent umbilical purulent discharge. She had undergone partial resection of the small intestine for obstruction and, later, a pyeloplasty for a stricture of the ureter-pyelo junction. Her younger brother had also undergone surgery for a urachal sinus 1 year earlier. She was found to have an umbilical granuloma with a fistulous track that could be probed for 3 cm distally. Computed tomography (CT) and ultrasonography confirmed the fistulous track. Under a diagnosis of urachal sinus, a urachal remnant was excised. Histological analysis of the excised specimen revealed only inflammatory granulomatous tissue with marked infiltration of lymphocytes and foreign body giant cells. Urachal cysts are associated with a risk of intestinal strangulation and therefore, the finding of urachal disease justifies detailed evaluation.