The optimal surgical care of patients with imperforate anus begins with appropriate decision making in the critical newborn period. In most cases the decision to create a colostomy should be delayed until the infant is 18 to 24 hours old. Except in cases of a rectoperineal fistula, most neonates are best treated with a completely divided left-lower-quadrant colostomy between the descending and sigmoid colons. Female patients with cloacal anomalies must be recognized at birth so that all urgent urologic evaluations can be performed. Hydrocolpos and obstructive uropathy are common in these neonates and warrant urgent decompression of the urinary tract with a vaginostomy and/or vesicostomy as well as a colostomy. Renal ultrasonography and voiding cystourethrography are mandatory for all patients regardless of the height of the defect. It is critical to discover the important precursors to renal insufficiency including renal agenesis, renal dysplasia, and vesicoureteral reflux in the neonate. The presence of these anomalies mandates early consultation with a pediatric urologist because the morbidity and mortality of these lesions often exceed those of the imperforate anus. Spinal cord anomalies are common and can be found even in patients who have normal plain films and low defects. Spinal ultrasonography or magnetic resonance imaging should be performed in all neonates to rule out occult spinal pathology such as tethered cord or lipoma of the cord. Efficacious and cost-effective care of patients with imperforate anus begins with a carefully thought out plan in the neonate. Optimal execution of the evaluation and surgical treatment at this phase sets the stage for the best possible outcome later in life.