Surgical repair involves creating an opening for passage of stool. Complete absence of an anal opening requires emergency surgery for the newborn.

Surgical repairs are done while the baby is deep asleep and pain-free (using general anesthesia).

Surgery for a high type imperforate anus defect usually involves creation of a temporary opening of the large intestine (colon) onto the abdomen to allow passage of stool (this is called a colostomy). The baby is allowed to grow for several months before attempting the more complex anal repair.

The anal repair involves an abdominal incision, loosening the colon from its attachments in the abdomen to allow it to be repositioned. Through an anal incision, the rectal pouch is pulled down into place, and the anal opening is completed. The colostomy may be closed during this stage or may be left in place for a few more months and closed at a later stage.

Surgery for the low type imperforate anus (which frequently includes a fistula) involves closure of the fistula, creation of an anal opening, and repositioning the rectal pouch into the anal opening.

A major challenge for either type of defect and repair is finding, using, or creating adequate nerve and muscle structures around the rectum and anus to provide the child with the capacity for bowel control.