Congenital Brain Defects: Signs, Treatments & Risk Factors

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Congenital brain defect refers to a brain disorder or abnormality that is present in infants at birth or develops during the fetal growth period. Brain development begins in the first week post conception and continues throughout the pregnancy. Any alterations in this process due to various genetic and environmental factors can contribute to structural brain abnormalities.

This post explains the signs, causes, risk factors, diagnosis, treatment, prevention, and long-term outlook of congenital brain defects in babies.

Types Of Congenital Brain Malformations

The following types of congenital brain defects are often seen in babies (1).

  • Chiari malformation is when the part of the brain called the cerebellar tonsils protrudes to the upper spine through the skull opening. This may increase the pressure on the spinal cord and brain, blocking the normal flow of cerebrospinal fluid (CSF).
  • Encephalocele is a neural tube defect that causes the brain to bulge out from the cranial cavity without being covered by skin or skull bone. This can result in hydrocephalus and infections. Surgical closure and CSF drainage are required to treat this condition.
  • Arachnoid cysts are common brain cysts present at birth and occur due to the splitting of the arachnoid membrane, a membrane that covers the brain. These cysts are fluid-filled and often require surgical treatment.
  • Anencephaly is caused by the absence of a major portion of the brain and skull. This is a type of neural tube defect (NTD).
  • Holoprosencephaly is a structural birth defect where the brain does not divide into two hemispheres.
  • Microcephaly is a condition when the brain fails to develop into its average size and remains small.
  • Megalencephaly is when the brain is larger than normal.

Signs And Symptoms Of Congenital Brain Defects

Signs and symptoms of congenital brain defects may vary depending on the type of defect. Growth and developmental delay are seen in most babies. However, some babies may not have any symptoms during early childhood, and it can be an incidental finding on MRI.

Common signs and symptoms seen in congenital brain defects may include (2):

  • Seizures
  • Developmental delays
  • Muscle weakness
  • Increased or decreased muscle tone
  • Large or small head size
  • Vision and hearing impairments
  • Bowel and bladder issues
  • Abnormal reflexes
  • Hydrocephalus (enlargement of the fluid-filled spaces of the brain)
  • Feeding difficulties

Babies with congenital brain abnormalities can also have associated cleft lip and palate, gastrointestinal defects, and cardiovascular defects. Babies with blocked CSF flow can develop hydrocephalus. Mild cases of Chiari malformations may not cause symptoms in early childhood, and it is often diagnosed later during MRI for headaches or other causes.

Risk Factors And Causes Of Congenital Brain Defects

There may not be a specific cause in most cases of congenital brain defects. However, various environmental and genetic factors are often linked to brain malformations (3) (4).

  • Inherited or sporadic genetic mutations
  • Trisomy 9 (having three copies of the ninth chromosome) is associated with Chiari II defects (involves displacement of the medulla of the brain and lumbosacral spinal myelomeningocele) and Dandy-Walker syndrome (underdeveloped cerebellum)
  • Trisomy 13 causes microcephaly and holoprosencephaly
  • Trisomy 13 and 18 may cause neural tube defects.
  • Prenatal bacterial and viral infections
  • Maternal drug and other substance use during pregnancy
  • Trauma to the fetus such as falling on the stomach during pregnancy

The following factors may increase the risk for congenital brain defects (4).

  • Certain medications and radiation
  • Nutritional deficiencies, including being deficient in folate while pregnant
  • Maternal diabetes
  • Phenylketonuria (PKU), a metabolic disorder
  • Traveling to areas with known infectious disease outbreaks and not getting the appropriate vaccines can increase the risk of maternal bacterial or viral infections

Maternal infections such as varicella-zoster, rubella, and herpes simplex can significantly increase the risk of congenital brain abnormalities in babies.

Diagnosis Of Congenital Brain Defects

Pediatric neurologists evaluate babies with suspected congenital brain malformations to diagnose and treat the problem. Physical examination, including the neurological examination and health history and brain imaging such as MRI scan, help to confirm the congenital brain anomalies. MRI scans help to visualize the brain malformations in most cases (1).

Cranial (head) ultrasound can help visualize newborns’ brains since their skull bones are not completely formed. Genetic testing of the baby and parents are often done in certain cases if a congenital brain anomaly is associated with genetic conditions.

Treatment For Congenital Brain Defects

Treatment options for brain defects may vary depending on the type and severity of the defect. Multidisciplinary approaches are often required to manage brain malformations. Geneticists, craniofacial plastic surgeons, neurosurgeons, and a few other specialists are often involved in the care.

Mild brain malformations that do not cause severe problems may not require specific treatment and are observed regularly. For children with moderate to severe brain malformations, the following treatments might be used to reduce symptoms (1).

  • Anticonvulsant or antiseizure medications to reduce seizure episodes
  • Chiari decompression surgery is done to widen the foramen magnum by removing bone to make space for the brain in the skull
  • Cranial surgeries to correct skull deformations help the brain to grow normally
  • Shunts are created in hydrocephalus to drain cerebrospinal fluid

Pediatric neurosurgeons schedule follow-up visits after surgical procedures to track the progress and recovery.

Outlook For Congenital Brain Defects

The prognosis of congenital brain defects may vary depending on the severity and type of brain defect. In addition, mental and physical impairment and environmental factors may contribute to the prognosis.

Minor neurological defects are present in most cases. However, people with minor defects can grow and function independently. Some brain defects can significantly disable a child and often limit their mental functioning to below average. Severe cases, such as anencephaly, can be fatal before or soon after birth.

Prevention Of Congenital Brain Defects

Some cases of congenital brain defects cannot be prevented. However, the following measures during pregnancy may reduce the risk of brain malformations in some babies (5).

  • Take daily recommended amount of folic acid before conception and during the pregnancy
  • Seek early prenatal care
  • Become up to date with vaccines, including the annual influenza vaccine (flu shot) during pregnancy
  • Try to reach a healthy weight before planning pregnancy
  • Keep chronic conditions, such as diabetes and hypertension, under control
  • Maintain a balanced and healthy diet, with adequate physical activities during pregnancy
  • Avoid harmful substances such as alcohol, tobacco, or recreational drugs during pregnancy

In addition to these tips, you may also make your house mosquito-proof. You must use mosquito repellants while traveling to areas with mosquito-borne illnesses, such as the Zika virus infection, that cause congenital brain malformations. Congenital malformations such as neural tube defects can be prevented with an adequate intake of prenatal vitamins that include folic acid.

Frequently Asked Questions

1. How common are congenital defects?

Every year, about 3 to 6% of babies around the world are born with a serious congenital anomaly (6). The surviving children could have a risk of disabilities.

2. What is the difference between genetic and congenital disorders?

A genetic disorder inherited from one or both parents may include congenital disabilities, chronic disorders, developmental issues, and sensory deficits (7). On the other hand, a congenital disorder/malformation refers to any structural or functional anomaly that occurs during fetal life and is identified before birth, at birth, or later in life (8).

A congenital brain defect can occur at birth or during fetal development, causing growth and developmental delays in most cases. In other cases, however, the brain abnormality may only be discovered through MRI scans. Treatment entails a multidisciplinary approach and is dependent on the nature and severity of the disorder. Babies with severe impairments may require various therapies and training to enhance their quality of life. In such cases, it is essential never to miss a scheduled follow-up and keep in touch with your child’s pediatrician.

Key Pointers

  • Congenital brain anomalies could be of many types.
  • Their common symptoms may include seizures, abnormal head size, or reflexes.
  • Genetic factors, maternal dietary deficits, or prenatal infections could all have a role in these birth abnormalities.
  • Doctors may diagnose congenital brain defects through MRI scans or an ultrasound of a newborn.


MomJunction's articles are written after analyzing the research works of expert authors and institutions. Our references consist of resources established by authorities in their respective fields. You can learn more about the authenticity of the information we present in our editorial policy.
1. Congenital Brain and Spine Malformations; Johns Hopkins Medicine
2. Brain defects and malformations of the brain; Pediatric Neurology; Cohen Children’s Medical Center- Northwell Health
3. Congenital Brain Malformations; UCSF Benioff Children’s Hospitals
4. Nervous System Malformations; U.S. National Library of Medicine
5. Overview of Congenital Neurologic Anomalies; MSD Manual
6. World Birth Defects Day 2022: Global Efforts to Prevent Birth Defects and Support Families; CDC
7. Genetic Disorders; Boston Children’s Hospital
8. Congenital Anomalies; WHO
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Dr. Jessica Madden

Jessica Madden is a pediatrician, neonatologist, lactation consultant, and mother of four, who has been taking care of newborns since 2001. She works as a neonatologist in the NICU at Rainbow Babies and Children’s Hospital in Cleveland, Ohio, and founded Primrose Newborn Care, a newborn medicine and “4th trimester” home-visiting and telemedicine practice, in 2018.  Dr. Madden is a Fellow... more

Dr Bisny T. Joseph

Dr. Bisny T. Joseph is a Georgian Board-certified physician. She has completed her professional graduate degree as a medical doctor from Tbilisi State Medical University, Georgia. She has 3+ years of experience in various sectors of medical affairs as a physician, medical reviewer, medical writer, health coach, and Q&A expert. Her interest in digital medical education and patient education made... more