The aim of this study was to evaluate role of anorectal manometry (ARM) and anal endosonography (ES) in assessment of the internal anal sphincter (IAS) quality on continence outcome following repair of anorectal anomalies (ARA). We devised a scoring system to evaluate the quality of the IAS based on ARM and ES and correlated the scores with clinical outcome, using a modified Wingfield score (MWS) for faecal continence. We also assessed the implication of megarectum and neuropathy on faecal continence. Of 54 children studied, 34 had high ARA and 20 had low ARA. Children with high ARA had poor sphincters on ES and ARM, and also poor faecal continence compared to those with low ARA. The presence of megarectum and neuropathy was associated with uniformly poor outcome irrespective of the IAS quality. The correlations between MWS on one hand, and ES and ARM scores for IAS on the other hand were weak in the whole study group, ES r = 0.27, P < 0.04, and ARM r = 0.39, P < 0.004. However, the correlations were strong in those who had isolated ARA without megarectum or neuropathy, ES r = 0.51, P < 0.02 and ARM r = 0.55, P < 0.01, respectively. In conclusion, the ARM and ES are valuable in evaluation of continence outcome in children after surgery for ARA and those with good quality IAS had better faecal continence. The IAS is a vital component in functional outcome in absence of neuropathy and megarectum.