Overview 

Encephalocele (pronounced “en-SEF-al-oh-SEEL”) is a rare congenital brain malformation, which is a herniation of brain tissue with or without meninges through a cranial fossa defect.¹ Classification is based on its location, and other congenital abnormalities are associated with it. 

Encephaloceles are rare to find globally, occurring in about one in five thousand live births and are most times associated with stillbirths at twenty weeks of gestation.² According to the Minnesota Department of Health, between 2014 - 2018, twenty-four babies were born with encephalocele, resulting in a rate of less than one baby per ten thousand births. Annually, about sixty-five babies are born with encephalocele.²

A large number of survivors of encephaloceles have significant cognitive defects. The type of defect is based on the structure of the brain, but motor and learning deficits are most common.

Early detection during pregnancy is carried out using ultrasound and is important for appropriate management and postnatal care.

Types of Encephalocele

Cleveland Clinic grouped encephalocele into four major categories, which are based on the location of the opening in the skull, namely: ³

• Frontoethmoidal (or Sincipital): Located close to the baby's forehead
• Sphenoidal: Located behind your baby's eyes and/or in front of the ears
• Parietal: Closest to the back of your baby's head
• Occipital: At the back of your baby’s skull near the neck region. It is the most common type of encephalocele

Associated Anomalies 

Occasional abnormalities associated with babies born with encephalocele:

• Hydrocephalus 
• Microcephalus 
• Meckel-Gruber syndrome often presents with multiple anomalies such as polydactyly, polycystic kidneys, brain defects like holoprosencephaly, eye malformations, retinal changes, and cardiac defects 
• Goldenhar's, or amniotic band
• Walker-Warburg

Commonly associated neurologic malformations include:

• Dandy-Walker syndrome 
• Agenesis of the corpus callosum
• Chiari malformation
• Craniosynostosis
• Myelomeningocele
• Lipomas of the corpus callosum
• Holoprosencephaly

Systemic associated malformation includes:

• Renal agenesis 
• Facial clefting 
• Syndactyly 
• Arm and rib anomalies

Prenatal Diagnostic Methods for Encephalocele 

Encephalocele can be diagnosed during pregnancy by your healthcare provider, either by recommending a Magnetic Resonance Imaging (MRI) or during a routine ultrasound.

Diagnosis confirmation occurs immediately when your baby is born by visual examination of your baby. Other tests can be recommended by your provider if it is suspected that your baby has encephalocele. They include:

• Cell-Free fetal DNA testing: A sample of your blood is taken to look for copies of fetal DNA. If copies of fetal DNA are found, then it means a positive result, and there could be a problem with your baby's DNA
• Amniocentesis: This is a prenatal test where your doctor collects a sample of the fluid surrounding your baby in the uterus, then analyses it for possible genetic abnormalities. It is carried out most often between the fifth to seventh months of pregnancy

Testing the baby: When your baby is born, a blood sample is taken to look for chromosomal abnormalities. 

Role of ultrasound in prenatal diagnosis⁵

Encephaloceles can sometimes be detected during the first trimester, particularly in an ultrasound performed between 11 and 14 weeks of pregnancy.

A cyst within a cyst appearance around the skull region is occasionally seen. This occurs when the fourth ventricle protrudes into the encephalocele and is encased in cerebrospinal fluid.

In a 2D ultrasound, an encephalocele appears as an opening in the skull with a sac bulging out, which may hold cerebrospinal fluid (meningocele) or parts of the brain (encephalocele).

Typical features include fluid-filled sacs that appear anechoic, areas of solid brain tissue, flattening of the base of the occiput, enlarged ventricles, and, at times, a ‘cyst-within-a-cyst’ pattern caused by herniation of CSF-filled ventricles.

Role of fetal MRI in prenatal diagnosis

Fetal MRI should be performed only after a high-quality fetal ultrasound examination.⁶ It is mostly recommended when more anatomical evaluation details are needed or when the ultrasound results are inconclusive. It is also used to differentiate small encephaloceles from other masses such as cysts or hemangiomas, etc.⁷

Fetal MRI is performed after the 18 - 20 gestation weeks when CNS structures are more reliable.⁸

Studies show disorganised brain tissue, brainstem anomalies, Chiari III features, and tract involvement in occipital meningoencephaloceles. Advanced techniques like diffusion-weighted imaging (DWI) and tractography enhance detail and facilitate syndrome recognition.⁹

A 2019 study published in the Journal of South Asian Federation of Obstetrics and Gynaecology reported that 13.7% of extra CNS anomalies were detected exclusively by MRI after being missed on ultrasound, while 18.2% were identified only after birth despite prenatal imaging.⁹

Early fetal MRI has some downsides to it, such as excessive fetal movement, the fetus being very small, and organs still forming. Advances in coil technology, including the use of higher-channel body or torso coils, combined with better MRI systems, now allow for a higher signal-to-noise ratio.⁹

Comparative Role of Ultrasound and MRI

Complementary nature

Ultrasound, particularly detailed mid-trimester neurosonography, serves as an easily accessible method for spotting encephaloceles during pregnancy. It helps identify the skull opening, determine whether the protrusion contains fluid or brain tissue, and check for other related anomalies. According to ISUOG guidelines, MRI is not the first choice but is used as a second tool only after a thorough ultrasound by a specialist and when extra detail is needed.^10,11

Fetal MRI becomes valuable when ultrasound cannot give a clear picture, such as in cases of maternal obesity, poor fetal positioning, or low amniotic fluid. It is also recommended when more detailed information about the brain is needed to guide counselling or delivery decisions, for example, to assess the amount of brain tissue involved, the condition of the posterior fossa, or the presence of anomalies like those affecting the corpus callosum or cortex.^12,13

Accuracy in prognosis

Where brain and central nervous system anomalies are involved, MRI often confirms what was seen during the ultrasound and provides extra details that can change the care plan. The Society for Maternal-Fetal Medicine highlights that MRI is particularly helpful for spotting subtle brain abnormalities that ultrasound might miss, and these findings play a key role in shaping prognosis and counselling.¹⁴

Being able to define the amount of brain tissue involved and identify other brain abnormalities, such as issues with the corpus callosum or brainstem, helps doctors give a more accurate prediction of the baby’s development and chances of survival. This makes counselling for parents much clearer.¹²

Clinical management after diagnosis

Genetic Testing: Offer amniocentesis with chromosomal analysis and microarray to check for genetic or syndromic conditions that affect prognosis.¹⁵

Counselling and Prognosis: Outcome depends on lesion size, skull opening location, brain involvement, and other anomalies. Multidisciplinary counselling helps parents understand survival chances and long-term outlook.¹⁵

Delivery Planning: Schedule delivery in a tertiary centre with neonatal and neurosurgical care. Cesarean section may be advised for large sacs to prevent rupture.¹⁵

Summary

Ultrasound serves as the essential first-line imaging modality in the early detection of encephaloceles because it is effective, accessible, and valuable.

Fetal MRI gives indispensable supplementary insight that ultrasound cannot give, especially for anatomical precision, syndrome detection, and enhanced counselling.

The combination of both enables more informed prenatal decisions, optimised perinatal planning, and improved overall care pathways for affected pregnancies.