Dr. Sarah Livelo 01 Mar 2022

Most children get sick from diseases and illnesses that they acquire as they grow up. However, there are medical conditions that develop even before a child is born. These are called congenital defects or diseases. These may cause further problems as children become older, such as infections, growth delay, and issues with neurodevelopment, which is why an early diagnosis and urgent treatment are critical in managing these conditions.

A significant number of congenital diseases require surgery. Fetal surgery is a good alternative, but is not easily accessible, especially in developing countries. This article will focus on congenital defects that are more commonly treated after birth or during infancy.

The most common type of congenital anomaly among surgical emergencies in newborns are gastrointestinal anomalies at 50%. Other significantly affected organs or organ systems are the heart, lungs, and the nervous system. For this article, congenital heart defects are not included, and are covered in a separate post.

Preoperative care

Before a newborn or infant undergoes surgery, medical evaluation should be done unless the condition is a medical emergency in itself. Healthcare providers may request for laboratory exams and imaging tests to ensure that the baby can tolerate the surgical procedure. Sometimes, antibiotics may be given to help prevent unwanted infections, since babies do not have a mature immune system yet.

Common Types of Surgery in Newborns and Infants

Esophageal Atresia and Tracheoesophageal Fistula

The esophagus is the connection between the mouth and the stomach and is the main passageway for food. On the other hand, the trachea is the connection between the upper airway (nose, including the mouth) and the lungs, and is the main passageway for air. During the first two months of pregnancy, a wall of tissue develops to separate the trachea and esophagus from each other. When the esophagus doesn’t form correctly, it can end up closed instead of connecting the mouth and the stomach. This is known as esophageal atresia. In some newborns, an abnormal connection between the esophagus and trachea can develop instead, called a tracheoesophageal fistula (TEF).

Both esophageal atresia and TEF can develop on their own or may be part of a combination of congenital defects (congenital syndrome). Examples include trisomies (like Down syndrome) and VACTERL syndrome. Infants who have esophageal atresia or TEF find it difficult to feed properly. They may cough, choke, vomit or even turn blue, especially during feeding time. Frothy, white bubbles may also be seen in the mouth, and for babies who need a gastric tube, healthcare providers may find it difficult or impossible to place one properly.

An x-ray is usually requested to confirm this condition. The main treatment option is surgery, and in certain cases, more than one surgery may be needed to fully correct the anatomical defects.

Cleft Lip and Palate

The roof of the mouth is made up of tissues forming parts of the nose, lips, and mouth that fuse at around the 4th to 10th week of pregnancy. If these tissues do not fuse properly, this can lead to openings (clefts) that create gaps in the lips, roof of the mouth, or even both. For every 500-2,500 newborns, one may be affected with this congenital condition.

While a cleft lip is easily seen at first glance, a cleft palate may be discovered when examining the mouth. Babies with cleft lip and/or palate can have problems with feeding, swallowing, and communicating words clearly (for older kids). In some cases, even hearing and dental health are also affected. Surgery is important in restoring the correct oral anatomy.

Omphalocele and Gastroschisis

Before birth, a fetus receives oxygen and nutrients through the umbilical cord, which contains a set of blood vessels connected to the mother’s placenta. Sometimes the abdominal wall doesn’t develop well and becomes weak, allowing not just blood vessels to pass through this cavity (the belly button), but also other parts of the gastrointestinal tract. If the intestines are seen outside the abdomen but covered in a thin layer of tissue, this condition is called omphalocele. If no layer covers the intestines, the condition is known as gastroschisis.

These two abdominal wall defects are only fully corrected via surgery. For some babies, there may be an underlying chromosomal anomaly or congenital syndrome. Thorough medical evaluation is needed in these cases.

Imperforate anus

We can trace the development of the anus as early as the second week after conception. The primitive gut tube forms the hindgut, which goes through various processes of development. By the 7th to 8th week of gestation, one part of the anal membrane (found in the hindgut) should open to form the anal opening. If this doesn’t happen, the anus doesn’t form — leading to an imperforate anus.

Babies with imperforate anus may present with constipation or lack of stools. Some newborns are born with no opening at all, but others develop a fistula to compensate for the lack of an anal opening. Fistulas typically form between the intestines (rectum) and another opening, such as the vaginal or urethral areas, to be able to excrete fecal waste. This condition may also be diagnosed through laboratory imaging, like x-rays and ultrasound.

Surgery is needed to create an anal opening, correct any fistulas (if present), and to manage any other anatomical defects due to the fistula formation.

Congenital Cystic Malformation (Congenital Pulmonary Airway Malformation)

Some congenital disorders occur when one type of tissue forms in an organ where it doesn’t typically grow. In congenital pulmonary airway malformation (CPAM), cysts containing unusual lung tissue (called dysplastic tissue) form in the lobes of the lungs. There are different types of CPAM depending on how extensive the dysplastic tissue is. Unfortunately, most CPAM types have a poor prognosis, either predisposing the child to malignancy or possible death during infancy.

Children with CPAM usually have difficulty breathing and recurrent respiratory infections. A chest x-ray may be done to confirm the diagnosis. Treatment is advised before the infant turns 1 year old. This involves removal of the affected lung tissue. At the same time, surgical intervention can also be used to check for any possible cancerous lung tissue in the patient.

Congenital Diaphragmatic Hernia

The diaphragm is a thin, wide muscle found beneath the lungs and above the stomach and intestines. Its main function is to assist in proper inhalation and exhalation of the lungs. For every 2,000-5,000 babies born alive, one newborn may not have a completely formed diaphragm, causing some parts of their gastrointestinal tract to move upwards into the lung cavity. This condition is called congenital diaphragmatic hernia (CDH).

This congenital defect could be diagnosed even before birth via a fetal ultrasound (as early as 4th to 6th months of gestation), depending on how large the hole is. If this condition is suspected before birth, special preparations are required during birth and delivery. Babies with CDH typically present with difficulty breathing properly right after birth. Their stomach may also look sunken while the chest may look much larger. A chest x-ray will confirm the diagnosis. Both respiratory support through mechanical ventilation (to ensure enough air reaches the lungs) and surgery (to repair the hole in the diaphragm) are needed.


The two main components of the nervous system are the brain and the spinal cord. These structures are covered by layers of tissue called meninges and are encased in specialized fluid (cerebrospinal fluid). One common congenital defect occurs when the spinal canal doesn’t completely close. Part of the spinal cord (including the meninges and cerebrospinal fluid) stick out through this defect, resulting in a sac-like mass over one area of the spine, usually found at the lower back, called a myelomeningocele.

Although it’s easy to see a sac-like mass, the diagnosis is usually confirmed even before a child is born, through either a prenatal ultrasound or a fetal MRI. After birth, additional imaging tests like x-rays and ultrasound may be done to find out critical details of the condition. Surgery is urgently done to prevent build-up of cerebrospinal fluid in the brain (leading to a hydrocephalus) and prevent any further neurological damage due to the defect.


Most surgeries done in newborns and infants are due to medical emergencies or urgent conditions. Frequently, congenital defects are at the top of the list for surgery in this age group, especially gastrointestinal anomalies. There are numerous medical conditions that would need surgical management, but this article focuses only on the most common surgical conditions, how they are typically diagnosed, and which diagnostic steps are done before surgery.

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About the Author:
Dr. Sarah Livelo is a licensed physician with specialty training in Pediatrics. When she isn't seeing patients, she delves into healthcare and medical writing. She is also interested in advancements on nutrition and fitness. She graduated with a medical degree from the De La Salle Health Sciences Institute in Cavite, Philippines and had further medical training in Makati Medical Center for three years.


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