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Objective To evaluate and compare the medium-term outcome between one-stage Pena operation and two-stage Pena operation as well as between Pena operation and anorectoplasty via abdominal perineal operation therapies high imperforate anus by retrospective review of operation methods and medium-term follow-up study.Methods This is a retrospective review of forty three cases who were underwent Pena operation at the children’s hospital of Chongqing Medical University from January in2005to December in2008.The clinical data of43cases with high imperforate anus, in which25cases with imperforate distance between2cm and3cm were treated one-stage Pena operation;18cases with imperforate distance above3cm were treated by colon stoma in neonate and then Pena operation was executed after6months.All of cases were followed after post-operation2years to5years.Sixty eight cases with high anorectal malformation were treated by anorectoplasty via abdominal perineal operation in Xinhua Hospital Affiliated Shanghai Second Medical University before1987.Postoperative follow-up data of the both Xinhua Hospital and our hospital were analysesed.Result Forty three cases follow-up2to5years growthed normally. In one-stage Pena operation group:19excellent、6good, two-stage Pena operation group:13excellent、5good according to the guide recommended by Chinese Medical Association of Pediatric Surgery Branch.68cases with high anorectal malformation were treated by anorectoplasty via abdominal perineal operation in Xinhua Hospital Affiliated Shanghai Second Medical University before1987and then follow-up9.5years. Clinical evaluation of the defecation function:excellent in29cases、good in17cases、poor in22cases. Com pared with Pena operation,with the result:the percentages of excellent and good rate increased from67.6%to100%(P<0.05).Conclusions Pena operation can be offered excellent results of the medium-term outcome for treating high imperforate anus.We suggest that two-stage Pena operation applying to treat the high imperforate anus of3cm above, were treated by colon stoma in neonate and then Pena operation was executed after6months.The cases with imperforate distance of below3cm or with poor general condition or with combined with other severe malformations and accompany fistula, we recommend two-stage operation.