Small intestine atresia means that there is a complete blockage or interruption somewhere in the course of the small intestine. Small intestine stenosis means that there is a narrowing of the passage within the small intestine. Surgery is often the best option for treating these conditions. During the procedure, the surgeon makes an incision in the abdomen to remove the affected part of the intestine, taking care to leave as much of a healthy intestine in place as possible. Then the surgeon reconnects your baby’s intestines.