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The majority of children with Hirschsprung disease (HD) after corrective surgery (CS) develop protracted defecation disorders (DDs) such as constipation, fecal incontinence, and/or enterocolitis. The aim of this investigation was to determine the diagnoses, therapies, and long-term clinical outcomes using a systematic algorithm to address protracted DD in children with HD after CS.Retrospective review of children with HD after CS cared for using a systematic algorithm at a tertiary care center. Potential anatomic etiologies were evaluated for first. Clinical outcome was categorized into 4 groups based on symptom severity, time interval from last enterocolitis episode, laxative usage, and/or rectal therapies at the time of last follow-up.Fifty-seven children were identified, of whom 51 (89.5%) had obstructive symptoms and/or enterocolitis and 6 (10.5%) had nonretentive fecal incontinence. Nonintractable constipation responsive to laxatives was identified in 10 (17.5%), colonic dysmotility in 4 (7.0%), nonrelaxing anal sphincter as a primary etiology in 22 (38.6%), bacterial overgrowth in 2 (3.5%), food intolerance in 2 (3.5%), and rapid transit in 2 (3.5%). Further surgical intervention was undertaken in 22 (38.6%), including 9 (15.8%) for residual aganglionosis. Mean follow-up was 41.4 ± 4.5 months. Clinical outcomes were excellent in 16 (28.1%), good in 22 (38.6%), fair in 1 (1.8%), and poor in 18 (31.6%). Children with enterocolitis were more likely to have an excellent or good clinical outcome.The majority of children with HD and protracted DD after CS have a favorable long-term clinical outcome when following a systematic algorithm.