We present the case of an Indian child with a high anorectal malformation (ARM) who postoperatively had troublesome fecal incontinence. Based on a dietary history, weight loss, and diarrhea, a duodenal biopsy was performed that revealed coeliac disease. Since being on a gluten-free diet, her symptoms have improved dramatically. To the best of our knowledge this is the first report in the English literature of such an association between ARMs and coeliac disease. Dietary modification alone can dramatically improve symptoms in these children.