← Back to Study Notes

Embryology & Developmental Anatomy

Anatomy
📅 Updated May 2026

Embryology & Developmental Anatomy

What Do You Need to Know?

  • Neurulation — ectoderm → neural plate → neural folds → neural tube; closure begins at the future cervical region (3rd–5th somite) and proceeds bidirectionally. Anterior neuropore closes day 25 (failure → anencephaly); posterior neuropore closes day 27–28 (failure → spina bifida).
  • Three primary vesicles (week 4): prosencephalon, mesencephalon, rhombencephalon → five secondary vesicles: telencephalon, diencephalon, mesencephalon, metencephalon, myelencephalon.
  • Neural crest = peripheral and autonomic nervous system + Schwann cells + sensory ganglia (DRG, CN V/VII/IX/X sensory) + adrenal medulla + melanocytes + odontoblasts + branchial arch derivatives.
  • Dysraphisms — spina bifida (occulta, meningocele, myelomeningocele), anencephaly. Folate before conception (0.4 mg/d, or 4 mg/d if prior NTD or VPA/CBZ exposure) reduces NTD risk ~70%. Maternal serum AFP elevated in open NTDs.
  • Posterior fossa malformations — Chiari I (tonsils ≥5 mm below foramen magnum), Chiari II (myelomeningocele + hindbrain herniation), Chiari III (encephalocele), Dandy-Walker (vermis hypoplasia + cystic 4th ventricle + enlarged posterior fossa).
  • Holoprosencephaly — failure of forebrain cleavage; ranges from alobar (severe, fused single ventricle, cyclopia) to lobar; associated with SHH pathway defects, trisomy 13, maternal diabetes.
  • Migration disorders — lissencephaly (smooth brain, no gyri; LIS1, DCX), heterotopia (periventricular nodular — filamin A, subcortical band — DCX females), polymicrogyria, schizencephaly.
  • Syringomyelia — CSF-filled cavity in spinal cord; classic association with Chiari I; “cape distribution” loss of pain/temperature (central cord crossing fibers); preserved fine touch/vibration.

Neurulation & Neural Tube Formation

Timing & Key Steps

Day / Week Event
Week 3 (day 18–22) Notochord induces overlying ectoderm → neural plate
Day 22–24 Neural folds form and elevate; fusion begins at the 3rd–5th somite level (future cervical region) and proceeds bidirectionally (cranial and caudal)
Day 25 Anterior (rostral) neuropore closes — failure causes anencephaly
Day 27–28 Posterior (caudal) neuropore closes — failure causes spina bifida (occulta to myelomeningocele depending on severity)
Week 4–5 Three primary vesicles (prosencephalon / mesencephalon / rhombencephalon)
Week 5 Five secondary vesicles (telencephalon / diencephalon / mesencephalon / metencephalon / myelencephalon)
Week 6–8 Pontine flexure forms 4th ventricle; cerebellar primordia develop
Week 8–16 Neural progenitor proliferation in the ventricular zone
Week 12–24 Radial neuronal migration (“inside-out” cortex — layer VI first, layer II last); myelination begins late 2nd trimester
Clinical Pearl — Folate & AFP

Maternal folate (0.4 mg/d preconception, 4 mg/d if prior NTD pregnancy or on valproate/carbamazepine/methotrexate) reduces NTD risk ~70% (MRC Vitamin Study). Maternal serum AFP is elevated in open NTDs (open spina bifida, anencephaly); closed NTDs (occulta, meningocele covered by skin) typically have normal AFP. Folate antagonists (valproate, carbamazepine, methotrexate, trimethoprim, sulfasalazine) increase NTD risk.

Brain Vesicles & Adult Derivatives
Primary Vesicle Secondary Vesicle Adult Derivatives Ventricular Cavity
Prosencephalon (forebrain) Telencephalon Cerebral hemispheres, cortex, white matter, basal ganglia (caudate, putamen, NA), amygdala, hippocampus, olfactory bulb (CN I) Lateral ventricles
Diencephalon Thalamus, hypothalamus, epithalamus (pineal, habenula), subthalamus, neurohypophysis (posterior pituitary), retina + optic nerve (CN II), globus pallidus* 3rd ventricle
Mesencephalon (midbrain) Mesencephalon Midbrain (tectum — superior + inferior colliculi; tegmentum — red nucleus, substantia nigra, CN III/IV nuclei); cerebral peduncles Cerebral aqueduct (of Sylvius)
Rhombencephalon (hindbrain) Metencephalon Pons + cerebellum Upper 4th ventricle
Myelencephalon Medulla Lower 4th ventricle + central canal

*Globus pallidus: classically taught as diencephalic; modern developmental data show it derives from the medial ganglionic eminence (telencephalic) but migrates ventrally. The board answer remains diencephalon.

Neural Crest Derivatives

Neural crest cells delaminate from the dorsal neural folds and migrate widely. Major derivatives:

  • Peripheral nervous system: all Schwann cells; sensory ganglia (DRG; sensory portions of CN V, VII, IX, X — mixed with placodal contribution)
  • Autonomic ganglia: sympathetic (paravertebral, prevertebral) and parasympathetic (including the enteric nervous system — failure of migration to distal colon → Hirschsprung disease)
  • Adrenal medulla (chromaffin cells)
  • Melanocytes (skin, hair, leptomeninges)
  • Odontoblasts; bones & cartilage of pharyngeal arches; mesenchyme of head and face
  • Aorticopulmonary septum + tunica media of arch-derived great vessels
  • Cranial leptomeninges (forebrain pia/arachnoid); caudal leptomeninges have mesodermal contribution
💎 Board Pearl — Neural Crest
  • CN VIII (vestibulocochlear) ganglia are from the OTIC PLACODE, not neural crest — classic board trap.
  • Sensory ganglia of CN V, VII, IX, X are mixed placode/neural crest derivation (proximal portions placodal, distal neural crest).
  • Neurocristopathies: neurofibromatosis 1, MEN 2A/2B, Hirschsprung, Waardenburg, DiGeorge, CHARGE, melanoma.

Neural Tube Defects (Dysraphisms)

Spectrum

Defect Description Maternal AFP Key Features
Spina bifida occulta Failure of posterior vertebral arches to close; meninges & cord remain intra-canal and skin-covered Normal Often asymptomatic; tuft of hair, dimple, lipoma, hyperpigmented patch over the lumbosacral area; may have tethered cord (urinary symptoms, weakness, scoliosis)
Meningocele Herniation of meninges (CSF-filled sac) through bony defect; spinal cord remains in canal Normal or mildly elevated Skin-covered or partially covered; cord typically intact; better prognosis than myelomeningocele
Myelomeningocele Herniation of meninges + neural tissue (spinal cord / cauda equina) through defect; open lesion Elevated ~80% lumbosacral; virtually always associated with Chiari II; 90% develop hydrocephalus; lower limb paralysis, bladder/bowel dysfunction. MOMS trial: prenatal repair improves motor outcomes
Anencephaly Failure of anterior neuropore closure (day 25) → absence of forebrain and calvarium Markedly elevated Incompatible with life; classic association with maternal folate deficiency and uncontrolled diabetes
Craniorachischisis Complete failure of neural tube closure → anencephaly + extensive open spina bifida along the entire length of the cord Very high Most severe end of the NTD spectrum; incompatible with life
Congenital dermal sinus Midline lumbosacral epithelium-lined tract extending from skin to dura (sometimes to cord); ~50% with associated dermoid/epidermoid Normal Skin dimple/sinus opening; recurrent meningitis (esp. Staphylococcus); abscess; tethered cord. Full surgical excision required — do NOT probe in clinic.
Diastematomyelia / Diplomyelia Longitudinal splitting of the spinal cord (Type I = bony spur dividing two dural sacs; Type II = single dural sac); associated with tethering, scoliosis, hair tuft Normal MRI for diagnosis; surgical untethering and spur removal if symptomatic
Encephalocele Herniation of brain and meninges through skull defect (most often occipital) Elevated Often syndromic (Meckel-Gruber); imaging shows herniated brain tissue through midline cranial defect
Clinical Pearl — Tethered Cord

Closed dysraphisms (occulta, lipomyelomeningocele, dermal sinus) can present years later as tethered cord syndrome: progressive lower-extremity weakness, back/leg pain, urinary incontinence, scoliosis. MRI shows the conus medullaris below L1–L2. Surgical detethering can prevent further neurologic decline.

Posterior Fossa Malformations
Malformation Anatomy Clinical Features
Chiari I Cerebellar tonsils ≥5 mm below foramen magnum; NO supratentorial malformation Often presents in adolescents/adults; suboccipital headache (worse with Valsalva), neck pain, downbeat nystagmus; syringomyelia in ~50% (cape distribution suspended sensory loss)
Chiari II (Arnold-Chiari) Vermis + brainstem + 4th ventricle herniation through foramen magnum (± tonsils); virtually always with myelomeningocele; small posterior fossa; tectal beaking Hydrocephalus (90%, often requires shunt); stridor, apnea, dysphagia, weak cry from lower brainstem dysfunction; cord-level deficits from myelomeningocele
Chiari III Chiari II features plus low occipital / high cervical encephalocele containing cerebellum and brainstem Rare; severe; high mortality
Dandy-Walker malformation Vermian hypoplasia/agenesis + cystic dilation of the 4th ventricle + enlarged posterior fossa with elevated tentorium / torcula Macrocephaly, hydrocephalus, developmental delay; ~50% have other CNS anomalies (corpus callosum agenesis); seizures common
Joubert syndrome “Molar tooth sign” on axial MRI (thickened elongated superior cerebellar peduncles + deep interpeduncular fossa + vermis hypoplasia) Ataxia, oculomotor apraxia, abnormal breathing pattern (hyperpnea-apnea), intellectual disability, retinal dystrophy — a ciliopathy

Forebrain Development Disorders — Holoprosencephaly

Holoprosencephaly (HPE) = failure of the prosencephalon to cleave into two cerebral hemispheres. Severity spectrum:

  • Alobar HPE — complete failure of cleavage; single ventricle / fused thalami; facial anomalies range up to cyclopia with proboscis; usually lethal
  • Semilobar HPE — partial separation posteriorly; intermediate severity; cleft lip/palate, hypotelorism
  • Lobar HPE — nearly normal separation with subtle midline fusion; mild facial dysmorphism; survivable
  • Middle interhemispheric variant (syntelencephaly) — failure of midline cleavage of posterior frontal/parietal regions only

Causes: sporadic; SHH (sonic hedgehog) pathway mutations (SHH, ZIC2, SIX3, TGIF); trisomy 13 (Patau); maternal diabetes; maternal alcohol use; cholesterol synthesis disorders (Smith-Lemli-Opitz). “Single midline maxillary central incisor” is a subtle marker.

Cortical Malformations & Migration Disorders
Disorder Mechanism Imaging / Pathology Clinical
Lissencephaly Type I (classic) Failure of neuronal migration; LIS1 (PAFAH1B1) on 17p13.3 or DCX (X-linked, females = subcortical band heterotopia) Smooth cortex with little/no gyration; thickened 4-layer cortex (vs normal 6-layer) Severe developmental delay, refractory epilepsy (including infantile spasms), feeding difficulty. Miller-Dieker syndrome = 17p13.3 contiguous deletion (LIS1 + YWHAE) with facial dysmorphism
Lissencephaly Type II (cobblestone) Overmigration through breached pial limiting membrane; dystroglycanopathies (Walker-Warburg, muscle-eye-brain, Fukuyama CMD); RELN/reelin mutations → lissencephaly with cerebellar hypoplasia Cobblestone cortical surface; eye abnormalities; muscular dystrophy Severe developmental delay, eye malformations, congenital muscular dystrophy
Periventricular nodular heterotopia Failure of neurons to leave the ventricular zone; FLNA (filamin A), X-linked dominant (lethal in males), affects females Subependymal gray-matter nodules lining lateral ventricles Often normal cognition; epilepsy in adolescence/adulthood; vascular abnormalities possible
Subcortical band heterotopia (“double cortex”) Partial arrest of migration; DCX (X-linked, females have band; males = lissencephaly) Smooth band of gray matter beneath cortex on MRI Epilepsy, intellectual disability of variable severity
Polymicrogyria Late migration/post-migrational disorder; many small abnormal gyri Excessive small gyri, irregular cortical surface; perisylvian most common pattern Bilateral perisylvian PMG: pseudobulbar palsy, epilepsy, intellectual disability
Schizencephaly Full-thickness cleft from ependyma to pia, lined by gray matter Open lip (CSF cleft) vs closed lip (apposed walls); often with absent septum pellucidum Hemiparesis, seizures, intellectual disability (severity depends on bilateral vs unilateral and open vs closed)
Hemimegalencephaly Unilateral hemispheric overgrowth with cortical dysplasia; somatic mosaic mTOR pathway (MTOR, AKT3, PIK3CA) Asymmetric hemispheric enlargement; cortical thickening; abnormal gyration Severe early-onset epilepsy, hemiparesis; surgical hemispherectomy is often curative for seizures
Focal cortical dysplasia (FCD) Blümcke/ILAE classification: Type I (lamination), Type IIa (dysmorphic neurons), Type IIb (balloon cells = mTORopathy), Type III (associated with adjacent lesion) MRI may show cortical thickening, blurred gray-white junction, “transmantle sign”; often MRI-negative Most common cause of medically refractory focal epilepsy in children leading to surgery; FCD IIb shares pathology with TSC cortical tubers

Other High-Yield Developmental Entities

Agenesis of the Corpus Callosum (ACC)

  • Failure of midline crossing of commissural fibers; can be complete or partial (posterior usually affected first because the corpus callosum develops front-to-back, EXCEPT for the rostrum which forms last)
  • Imaging hallmarks: Probst bundles (longitudinal white-matter tracts running anteroposteriorly along the medial hemispheric walls), colpocephaly (enlarged occipital horns), parallel orientation of lateral ventricles (“racing-car” sign)
  • May be isolated (often normal cognition) or syndromic (Aicardi syndrome — X-linked dominant, female predominant, infantile spasms + chorioretinal lacunae + ACC)

Septo-Optic Dysplasia (de Morsier)

  • Triad (any two of three required): optic nerve hypoplasia + absent septum pellucidum + hypothalamic-pituitary insufficiency
  • Associations: HESX1, SOX2, SOX3, OTX2 (PAX6 is for aniridia, NOT SOD); GH deficiency, ACTH/cortisol deficiency, central DI

Congenital Aqueductal Stenosis

  • Most common cause of congenital obstructive (non-communicating) hydrocephalus in infants — narrowing or web within the cerebral aqueduct of Sylvius prevents 3rd→4th ventricle CSF flow.
  • X-linked recessive forms (L1CAM) account for some cases — “HSAS” (hydrocephalus due to stenosis of aqueduct of Sylvius), males more affected. Other causes: in-utero infection (CMV, toxoplasmosis), tectal glioma, post-hemorrhagic gliosis.
  • Presentation: macrocephaly, bulging fontanelle, “sun-setting” eyes (Parinaud-like dorsal midbrain compression), developmental delay. Treatment: ETV (endoscopic third ventriculostomy) preferred when feasible, otherwise VP shunt.

Spinal Cord: Basal vs Alar Plate Derivatives

  • By week 4–5, the neural tube wall organizes around a sulcus limitans into two longitudinal columns:
  • Basal plate (ventral)motor neurons (anterior horn cells of the cord and motor cranial nerve nuclei).
  • Alar plate (dorsal)sensory interneurons (posterior horn of the cord and sensory cranial nerve nuclei).
  • The same alar/basal plate organization persists in the brainstem, where the sulcus limitans separates motor (medial) from sensory (lateral) cranial nerve nuclei in the floor of the 4th ventricle.

Cortical Architecture & Myelination Timing

  • Six-layered neocortex (from pia inward): I = molecular (Cajal-Retzius cells); II = external granular; III = external pyramidal; IV = internal granular (main thalamocortical input); V = internal pyramidal (corticospinal/Betz output); VI = multiform (corticothalamic output).
  • Migration is “inside-out” — layer VI forms first, layer II last (preplate → Cajal-Retzius/marginal zone + subplate → layers VI→II form sequentially).
  • Myelination: begins in the PNS in the first trimester, in the CNS from ~14 weeks; complete in the PNS by ~3–5 years; CNS myelination continues into the third decade (frontal cortex last). Order: caudal→rostral and central→peripheral within the brain; U-fibers myelinate LAST.
  • U-fiber rule: in most congenital leukodystrophies (MLD, X-ALD, Krabbe, PKU, MSUD) U-fibers are spared initially; U-fibers are involved early in Canavan disease, Alexander disease, and in acquired demyelinating processes (MS, ADEM, PML) — a board-classic discriminator.
  • Full-term infant nerve conduction velocities are ~50% of adult values; reach adult speeds by ~3–5 years (paralleling PNS myelin completion). Slow infant NCS is therefore normal — interpret cautiously against age-matched norms.

Syringomyelia

  • CSF-filled cavity (syrinx) within the central spinal cord
  • Classic association: Chiari I (~50%); also post-traumatic, post-inflammatory (TM), tumor-associated
  • Classic exam: “cape distribution” suspended sensory loss of pain & temperature (decussating spinothalamic fibers crossing the central cord are affected first) with preserved fine touch, vibration, and proprioception (dorsal columns spared); LMN weakness at the level of the syrinx (anterior horn involvement); UMN signs below as the syrinx enlarges and compresses the corticospinal tracts
  • MRI shows the syrinx; always image the craniocervical junction to evaluate for Chiari I

Board Pearls — Embryology Synthesis
💎 Must-Know Embryology Facts
  • Anterior neuropore closes day 25; posterior day 27–28. Anterior failure → anencephaly; posterior failure → spina bifida. Maternal AFP elevated only in open NTDs.
  • Folate 0.4 mg/d preconception; 4 mg/d if prior NTD or VPA/CBZ exposure → ~70% NTD risk reduction.
  • Neural crest = “PNS, melanocytes, adrenal medulla, branchial arch.” Hirschsprung = enteric crest failure. CN VIII is from otic placode, NOT neural crest.
  • Chiari I: tonsils ≥5 mm below foramen magnum; presents adolescent/adult; ~50% have syrinx. Chiari II: vermis + brainstem + 4th ventricle herniation; always with myelomeningocele; needs shunt 90%.
  • Holoprosencephaly: SHH pathway, trisomy 13, maternal diabetes; cyclopia in alobar.
  • Lissencephaly Type I = LIS1 / DCX (smooth brain, thick 4-layer cortex). Type II = cobblestone = dystroglycanopathies + RELN (overmigration).
  • FCD IIb has balloon cells and shares pathology with cortical tubers of TSC (mTORopathy).
  • Syringomyelia + cape distribution dissociated sensory loss + Chiari I = single board vignette pattern.

References

  1. Sadler TW. Langman’s Medical Embryology. 14th ed. Wolters Kluwer; 2018.
  2. Adam MP, Feldman J, Mirzaa GM, eds. GeneReviews® (Lissencephaly, Periventricular Heterotopia, Holoprosencephaly, Chiari, Joubert). University of Washington; 2022 updates.
  3. Barkovich AJ, Raybaud C. Pediatric Neuroimaging. 6th ed. Wolters Kluwer; 2018.
  4. Blümcke I, Thom M, Aronica E, et al. The clinicopathologic spectrum of focal cortical dysplasias: a consensus classification proposed by an ad hoc Task Force of the ILAE Diagnostic Methods Commission. Epilepsia. 2011;52(1):158–174.
  5. Adzick NS, Thom EA, Spong CY, et al. A randomized trial of prenatal versus postnatal repair of myelomeningocele (MOMS). N Engl J Med. 2011;364(11):993–1004.
  6. Ropper AH, Samuels MA, Klein JP, Prasad S. Adams and Victor’s Principles of Neurology. 12th ed. McGraw-Hill; 2023.