Funnel anus (FA) is a rare and distinct type of anorectal malformation characterized by a skin-lined deep anal funnel, missing transitional epithelium and stenosis secondary to fibrotic internal sphincter. We aimed to characterize associated anomalies, surgical management and outcome of children with FA. The hospital records of 11 consecutive children (7 boys) treated for FA between 1992 and 2006 were screened. The collected data included the type of anorectal malformation, surgical management, associated anomalies, results of diagnostic investigations and outcome. Only one patient was free of any associated malformation. Six patients had a complete Currarino syndrome. Seven patients had a hemisacrum (scimitar) and tethered cord was present in two cases. Six patients underwent excision of a benign presacral teratoma. Anal stenosis associated with FA was managed by serial dilatations. Subsequent resection of the megarectosigmoid secondary to refractory constipation was performed on five occasions. Three patients underwent coloanal pull-through for Hirschsprung's disease (HD). The level of aganglionosis was at the rectosigmoid junction in two cases and low in the rectum in one. One additional patient had hypoganglionosis. Of the three patients with HD two also had Down's syndrome. After median follow-up of 6.5 (0.3-13.5) years four patients have normal bowel function and four suffer from soiling. Two patients with HD and Down's syndrome and one patient with an undefined syndrome are fecally incontinent. Associated anomalies are common and diverse in children with FA. Pelvic MRI, sacral radiography, evaluation of the urinary tract and rectal biopsies are recommended as routine investigations in cases of FA. Surgical care of these patients is demanding and should be confined to dedicated centers.