Encephalocele is an NTD characterized by a pedunculated or sessile cystic, skin-covered lesion protruding through a defect in the cranium (skull bone). Encephaloceles can contain herniated meninges and brain tissue (encephalocele or meningoencephalocele) or only meninges (cranial meningocele).

Fig. 5. Encephalocele

Photograph sources: CDC–Beijing Medical University collaborative project; Dr Jaime Frias

Key findings in encephalocele (see Fig 5):
  1. Location – the midline defect will vary in location and size; the most common location is occipital (~74%), followed by parietal (13%).
  2. Covering – encephalocele is skin covered (unless a rupture has occurred).
  3. Herniation – may contain meninges and brain tissue (encephalocele) or meninges only (cranial meningocele).


Prenatal. Encephalocele might be diagnosed prenatally using ultrasound but should always be confirmed postnatally. Use programme rules (SOPs) to decide whether to accept or not accept prenatal diagnoses without postnatal confirmation (e.g. in cases of termination of pregnancy or unexamined fetal death).

Postnatal. The newborn examination, x-ray and magnetic resonance imaging (MRI) or computed tomography (CT) confirm the diagnosis and will distinguish it from the other anomalies that may involve the brain and cranium.

Clinical and epidemiologic notes

Approximately 20% of infants with encephalocele will have at least one additional unrelated major birth defect:
  • Polydactyly and/or renal anomalies.
  • May co-occur with Dandy-Walker malformation or Chiari malformation.
  • Can occur with many single genes disorders (e.g., Meckel-Gruber syndrome) and with some chromosomal anomalies (e.g., trisomy 13, trisomy 18).
Additional clinical tips:
  • Always look for additional anomalies and syndromes.
  • Note encephalocele location and size, and document if meninges and brain are herniated.
  • Check if amniotic bands are mentioned – encephalocele might be confused with the amniotic band spectrum. The occurrence of other findings (facial schisis, limb and ventral wall anomalies, bands) points towards the diagnosis of amniotic band spectrum.

Checklist for high-quality reporting

Encephalocele – Documentation Checklist
Describe in detail:
  • Defect location – occipital, frontal, nasal, parietal, etc.
  • Extent – size and whether brain is present in the sac.
  • Skin covering – it is expected with encephalocele (but could be ruptured).
  • Other anomalies – internal and external anomalies, including polydactyly, renal anomalies, etc.
  • Cephalohematoma or caput succedaneum (benign scalp swelling) – can be confused with encephalocele.
  • Amniotic bands or limb-body wall anomalies – check if present and if so, describe

Take and report photographs: Show clearly  the cranial lesion; can be crucial for review

Describe evaluations to find or rule out related and associated anomalies: 

  • Head circumference might be small – do not code as microcephaly.
  • Hydrocephalus might be present – do not code as hydrocephalus.
  • Genetic or chromosomal testing performed, where available.
  • Specialty consultations and surgical reports.

Report whether autopsy (pathology) findings are available and if so, report the results.