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Background: Patients with anorectal malformation (ARM) need long-term follow-up, in order to evaluate fecal continence; the main predictors of longer-term success are the type of ARM, associated anomalies and sacral integrity. Three-Dimensional High Resolution Anorectal Manometry (3D-HRAM) gives detailed information on pressure on the anal complex profile. Our objective was to analyze anal sphincter activity in ARM patients with 3D-HRAM establishing the correlation between manometric and clinical data. Methods: Forty ARM patients were submitted to 3D-HRAM: manometric, anatomical and clinical scores were correlated with each other and with the bowel management response (BM). Results: A positive correlation between all scores and types of ARM was found: in high ARM and in patients with spinal anomalies (regardless to ARM type) lower scores were reported and even after BM they did not achieve good continence. Conclusions: 3D-HRAM gives detailed data on the functional activity of the anal sphincter complex. Our study revealed a correlation between manometric parameters and clinical outcomes, confirming spinal malformations and ARM type as the most important prognostic risk factors for a bad outcome. Specific sphincteric defects can also be explored with manometry, allowing for tailored bowel management strategies.