BGDB Gastrointestinal - Early Embryo

From Embryology
Practical 1: Trilaminar Embryo | Early Embryo | Late Embryo | Fetal | Postnatal | Abnormalities | Lecture | Quiz

We have now reached the end of Week 4 and beginning of 5 of development. Start by looking briefly at the overview of the Carnegie stage 13 embryo GIT from one end to the other.

Then work through the listed specific serial sections of the embryo identifying the GIT features. Alternatively step through the serial sections yourself identifying the tract, its associated mesentries, organs and spaces.

Tract Development

The early developing gastrointestinal tract The later developing gastrointestinal tract
Early Embryo Later Embryo

Carnegie Stage 13 (Week 4-5)



Stage13 bf1.jpg Stage13 sem1.jpg
The individual serial slices have also been incorporated into a 3D model of this embryo.
Stage 13 - Gastrointestinal Tract
Section Name Description
Stage 13 image 057.jpg

Stage 13 image 058.jpg




Head arches cartoon.jpg Note how in this region it is arched over and cut twice in this section.

The righthand side towards the buccopharyngeal membrane, the lefthand side descending into the embryo body. Stage13 B2 excerpt.gif

Central region is the floor of pharynx formed by fusion of 3rd pharyngeal arches = hypopharyngeal eminence (precursor of root of tongue).

Rathke's pouch forming the rudimentary adenohypophysis (anterior pituitary).

Stage 13 image 059.jpg B3L Laryngeal tracheal groove - beginning of ventral compression, at 90 degrees to the lateral plane of the pharynx above this point.

Rudimentary thyroid ventral to aortic sac (also seen in B2, ventral to the hypopharyngeal eminence).

Stage 13 image 060.jpg B4L Laryngeal tracheal groove - Caudal pharynx compressed dorsoventrally.

Note that it lies between the aortic sac (ventrally) directly above the heart and the paired vessels of arch artery 6 and the dorsal aortas. The pale staining region behind these blood vessels is where the vertebral column will form.

Stage 13 image 061.jpg B5L Laryngopharynx - now compressed dorsoventrally between the paired arch artery 6 vessels.
Stage 13 image 063.jpg B7L Glottis - initial separation of the oesophagus (dorsal) from the trachea (ventral).

Note that this is occurring at the level of the heart atria.

Nasal placodes. Pulmonary arteries.

Stage 13 image 064.jpg C1L Gastrointestinal tract oesophagus (dorsal) is now separate from the respiratory trachea (ventral).
Stage 13 image 065.jpg C2L Oesophagus and trachea both surrounded by dense mesenchyme.

Right nasal pit.

Stage 13 image 066.jpg

Stage 13 image 067.jpg



Oesophagus and trachea both surrounded by dense mesenchyme.

Common cardinal vein in the posterior wall of the intraembryonic coelom.

The pleuropericardial folds which contribute later to the formation of the pleura and pericardium.

In C4, junction of right common cardinal vein with dorsal wall of sinus venosus.

Left nasal pit.

Stage 13 image 068.jpg C5L Smaller oesophagus and expanding trachea, this is also the upper region of the lung buds.

The ventral anchoring of attachment site is at the most cranial extension of the septum transversum. This attachment now divides the intraembryonic coelom around the trachea into two canals, the left and right pleuro (pericardio-peritoneal) canals.

Canals are lined by coelomic mesothelium and are continuous with whole intraembryonic coelom (they will be referred to hereafter simply as coelomic canals).

The pleuroperitoneal fold on the medial side of the right common cardinal vein will form part of the diaphragm.

Stage 13 image 069.jpg C6L Trachea expanded and beginning to bifurcate to the major bronchial branches for each lung.

Lateral extension of pulmonary mesenchyme is moulded to shape of coelomic canals. Oesophagus lumen obliterated (common site of oesophageal atresia and/or tracheo-oesophageal fistula). Prominent R pleuroperitoneal fold.

Stage 13 image 070.jpg C7L Trachea bifurcated to the major bronchial branches for each lung.

Note dorsal extent of coelomic canals.

Oesophagus lumen reappears caudal to bifurcation.

Distinct R (smaller on L) pleuroperitoneal fold below the common cardinal vein.

Stage 13 image 071.jpg D1L Oesophagus/stomach junction.

Right lung bud bronchus still visible, left bronchus ends above this section. Note the oesophagus now lies in the midline between the 2 bronchi.

Coelomic canals.

Stage 13 image 072.jpg D2L Ovoid stomach with developing space of the lesser sac on R.

Dorsal and ventral attachments of the mesenchyme are now known as dorsal and ventral mesogastria. Coelomic canals.

Stage 13 image 073.jpg D3L Rotation of stomach (seen from above) to right side.

Note change in outline of coelomic canals due to presence of liver.

Lesser sac. Note thick mesothelium lining the coelom along left edge of stomach, the primordium of the spleen and greater omentum along greater curvature.

Liver embedded in septum transversum (ventral border of septum transversum contributes to diaphragm).

Stage 13 image 074.jpg D4L Rotation of stomach (seen from above) to right side.

Ventral mesogastrium - Stomach is attached ventrally to the liver. (note the position of the ductus venosus)

Dorsal mesogastrium - within this structure the spleen will begin to form and later the greater omentum.

Peritoneal spaces - identify greater and lesser sac.

Stage 13 image 076.jpg D6L Pyloric region of stomach.

Ventral mesogastrium - Stomach is closely attached ventrally to the liver.

Dorsal mesogastrium - within this structure the spleen will begin to form and later the greater omentum.

Peritoneal spaces - identify greater and lesser sac.

Stage 13 image 081.jpg E4L Midgut.

Region close to the umbilicus. Note the close associated portal vein and the paired placental (umbilical) veins.

Stage 13 image 085.jpg F1L Midgut.

Looping out of body wall ventrally (cut tangentially).

Also note the righthand side hindgut region.

Stage 13 image 098.jpg G7L Caudal pharynx (extending laterally, ventral to dorsal aorta - cf B4). Stomach, mesentery
Stage 13 image 097.jpg G6L Narrow oesophagus. Tracheal bifurcation dorsal to sinus venosus.

Peritoneal Cavity

  • Fusion of the two separate intra-embryonic coelom spaces.
  • Intestinal loss of ventral attachment, except at the level of the stomach, dorsal attachment becomes true mesentery.

Stomach Development

The stomach initially appears at this stage (5 weeks) as a dilatation of the GIT in the foregut, which over the next 2 weeks will continue to expand to a fusiform structure and differential growth will it rotate in both the longitudinal and the horizontal planes.

<html5media height="520" width="490">File:Stomach rotation 01.mp4</html5media>

Click Here to play on mobile device

Differential growth of the ventral and dorsal stomach walls leads to establishing a lesser and greater curvature.


  • Yellow - endoderm and splanchnic mesoderm of stomach.
  • Red - mesentry (ventral at front and dorsal at back). The dorsal mesogastrium will form the greater omentum and the ventral mesogastrium will form the lesser omentum.
  • Blue - vagus nerve branches (left and right). A 90 degree rotation (during week 7) brings the left vagus anteriorly (to the front) and carries the right vagus posteriorly (to the back).

These combined rotations position the stomach in its adult orientation and movement of the mesenteries also moves the developing liver to the right and generates the greater omentum and lesser sac (see animations below).

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Lesser Sac Development

Development of Lesser Sac Development of Greater Omentum
Lesser sac 01 icon.jpg Greater omentum 001 icon.jpg
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Key: Yellow - endoderm of stomach. Orange - liver developing in ventral mesogastrium. Red - spleen developing in dorsal mesogastrium.

Note the narrow tubular connection between the intestinal loop and the yolk sac.

Gastrointestinal Tract Movies  
Mesoderm 001 icon.jpg
 ‎‎Week 3 Mesoderm
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Week3 folding icon.jpg
 ‎‎Week 3
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Amnion 001 icon.jpg
 ‎‎Amniotic Cavity
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Endoderm 002 icon.jpg
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Stomach rotation 01 icon.jpg
 ‎‎Stomach Rotation
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Gastrointestinal tract growth 01 icon.jpg
 ‎‎Tract Growth
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Greater omentum 001 icon.jpg
 ‎‎Greater Omentum
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Lesser sac 01 icon.jpg
 ‎‎Lesser sac
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Urogenital septum 001 icon.jpg
 ‎‎Urogenital Septum
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 ‎‎GIT Stage 13
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 ‎‎GIT Stage 22
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Stage23 MRI S04 icon.jpg
 ‎‎Sagittal GIT
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 ‎‎GIT Motility
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Gastroschisis 01.jpg
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Omphalocele 01 icon.jpg
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Stage 13 (week 5) Stage 22 (week 8) Stage 23 (week 8) GIT Abnormalities Ultrasound

Practical 1: Trilaminar Embryo | Early Embryo | Late Embryo | Fetal | Postnatal | Abnormalities | Lecture | Quiz

Related Terms

  • coelom - (Greek, koilma = cavity) Term used to describe a fluid-filled cavity or space. Placental vertebrate development have both extraembryonic (outside the embryo) and intraembryonic (inside the embryo) coeloms. The extraembryonic coeloms include the yolk sac, amniotic cavity and the chorionic cavity. The initial single intraembryonic coelom located in the lateral plate mesoderm will form the 3 major body cavities: pleural, pericardial and peritoneal.
  • greater omentum - A peritoneal fold of splanchnic mesoderm extending from the greater curvature of the stomach and hanging ventrally down "like an apron" in the peritoneal cavity over the small intestine. It forms initially in the embryo and fetus as a loop of the dorsal mesentery, which later fuses to form a single sheet attached to the posterior body wall. The lesser omentum is a smaller ventral peritoneal fold extending from lesser curvature of the stomach to liver.
  • lesser omentum - The smaller peritoneal fold of splanchnic mesoderm extending from lesser curvature of the stomach to liver formed from the ventral mesentery at this level of the gastrointestinal tract. The second larger greater omentum extends from the greater curvature of the stomach and hanging down "like an apron" ventrally over the small intestine.
  • lesser sac - (bursa omentalis, omental bursa) opening into the space behind the stomach and on the side of the lesser curvature.
Gastrointestinal Tract Terms  
  • allantois - An extraembryonic membrane, endoderm in origin extension from the early hindgut, then cloaca into the connecting stalk of placental animals, connected to the superior end of developing bladder. In reptiles and birds, acts as a reservoir for wastes and mediates gas exchange. In mammals is associated/incorporated with connecting stalk/placental cord fetal-maternal interface.
  • amnion - An extra-embryonic membrane, ectoderm and extraembryonic mesoderm in origin, also forms the innermost fetal membrane, that produces amniotic fluid. This fluid-filled sac initially lies above the trilaminar embryonic disc and with embryoic disc folding this sac is drawn ventrally to enclose (cover) the entire embryo, then fetus. The presence of this membrane led to the description of reptiles, bird, and mammals as amniotes.
  • amniotic fluid - The fluid that fills amniotic cavity totally encloses and cushions the embryo. Amniotic fluid enters both the gastrointestinal and respiratory tract following rupture of the buccopharyngeal membrane. The late fetus swallows amniotic fluid.
  • atresia - is an abnormal interruption of the tube lumen, the abnormality naming is based upon the anatomical location.
  • buccal - (Latin, bucca = cheek) A term used to relate to the mouth (oral cavity).
  • bile salts - Liver synthesized compounds derived from cholesterol that function postnatally in the small intestine to solubilize and absorb lipids, vitamins, and proteins. These compounds act as water-soluble amphipathic detergents. liver
  • buccopharyngeal membrane - (oral membrane) (Latin, bucca = cheek) A membrane which forms the external upper membrane limit (cranial end) of the early gastrointestinal tract. This membrane develops during gastrulation by ectoderm and endoderm without a middle (intervening) layer of mesoderm. The membrane lies at the floor of the ventral depression (stomodeum) where the oral cavity will open and will breakdown to form the initial "oral opening" of the gastrointestinal tract. The equivilent membrane at the lower end of the gastrointestinal tract is the cloacal membrane.
  • celiac artery - (celiac trunk) main blood supply to the foregut, excluding the pharynx, lower respiratory tract, and most of the oesophagus.
  • cholangiocytes - epithelial cells that line the intra- and extrahepatic ducts of the biliary tree. These cells modify the hepatocyte-derived bile, and are regulated by hormones, peptides, nucleotides, neurotransmitters, and other molecules. liver
  • cloaca - (cloacal cavity) The term describing the common cavity into which the intestinal, genital, and urinary tracts open in vertebrates. Located at the caudal end of the embryo it is located on the surface by the cloacal membrane. In many species this common cavity is later divided into a ventral urogenital region (urogenital sinus) and a dorsal gastrointestinal (rectal) region.
  • cloacal membrane - Forms the external lower membrane limit (caudal end) of the early gastrointestinal tract (GIT). This membrane is formed during gastrulation by ectoderm and endoderm without a middle (intervening) layer of mesoderm. The membrane breaks down to form the initial "anal opening" of the gastrointestinal tract.
  • coelomic cavity - (coelom) Term used to describe a space. There are extra-embryonic and intra-embryonic coeloms that form during vertebrate development. The single intra-embryonic coelom forms the 3 major body cavities: pleural cavity, pericardial cavity and peritoneal cavity.
  • crypt of Lieberkühn - (intestinal gland, intestinal crypt) intestinal villi epithelia extend down into the lamina propria where they form crypts that are the source of epithelial stem cells and immune function.
  • duplication - is an abnormal incomplete tube recanalization resulting in parallel lumens, this is really a specialized form of stenosis. (More? Image - small intestine duplication)
  • esophageal - (oesophageal)
  • foregut - first embryonic division of gastrointestinal tract extending from the oral (buccopharyngeal) membrane and contributing oesophagus, stomach, duodenum (to bile duct opening), liver, biliary apparatus (hepatic ducts, gallbladder, and bile duct), and pancreas. The forgut blood supply is the celiac artery (trunk) excluding the pharynx, lower respiratory tract, and most of the oesophagus.
  • galactosemia - Metabolic abnormality where the simple sugar galactose (half of lactose, the sugar in milk) cannot be metabolised. People with galactosemia cannot tolerate any form of milk (human or animal). Detected by the Guthrie test.
  • gastric transposition - clinical term for postnatal surgery treatment for esophageal atresia involving esophageal replacement. Typically performed on neonates between day 1 to 4. (More? gastrointestinal abnormalities | PMID 28658159
  • gastrointestinal divisions - refers to the 3 embryonic divisions contributing the gastrointestinal tract: foregut, Midgut and hindgut.
  • gastrula - (Greek, gastrula = little stomach) A stage of an animal embryo in which the three germ layers (endoderm/mesoderm/ectoderm) have just formed. All of these germ layers have contributions to the gastrointestinal tract.
  • gastrulation - The process of differentiation forming a gastrula. Term means literally means "to form a gut" but is more in development, as this process converts the bilaminar embryo (epiblast/hypoblast) into the trilaminar embryo (endoderm/mesoderm/ectoderm) establishing the 3 germ layers that will form all the future tissues of the entire embryo. This process also establishes the the initial body axes. (More? gastrulation)
  • Guthrie test - (heel prick) A neonatal blood screening test developed by Dr Robert Guthrie (1916-95) for determining a range of metabolic disorders and infections in the neonate. (More? Guthrie test)
  • heterotaxia - (Greek heteros = different; taxis = arrangement) is the right/left transposition of thoracic and/or abdominal organs.
  • hindgut - final embryonic division of gastrointestinal tract extending to the cloacal membrane and contributing part of the transverse colon (left half to one third), descending colon, sigmoid colon, rectum, part of anal canal (superior), urinary epithelium (bladder and most urethra). The hindgut blood supply is the inferior mesenteric artery.
  • inferior mesenteric artery - main blood supply to the hindgut
  • intestine - (bowel) part of the gastrointestinal tract (GIT) lying between the stomach and anus where absorption of nutrients and water occur. This region is further divided anatomically and functionally into the small intestine or bowel (duodenum, jejunum and ileum) and large intestine or bowel (cecum and colon).
  • intestinal perforation - gastrointestinal abnormality identified in neonates can be due to necrotizing enterocolitis, Hirschsprung’s disease or meconium ileus.
  • intraembryonic coelom - The "horseshoe-shaped" space (cavity) that forms initially in the third week of development in the lateral plate mesoderm that will eventually form the 3 main body cavities: pericardial, pleural, peritoneal. The intraembryonic coelom communicates transiently with the extraembryonic coelom.
  • meconium ileus intestine obstruction within the ileum due to abnormal meconium properties.
  • mesentery - connects gastrointestinal tract to the posterior body wall and is a double layer of visceral peritoneum.
  • mesothelium - The mesoderm derived epithelial covering of coelomic organs and also line their cavities.
  • Midgut - middle embryonic division of gastrointestinal tract contributing the small intestine (including duodenum distal bile duct opening), cecum, appendix, ascending colon, and part of the transverse colon (right half to two thirds). The midgut blood supply is the superior mesenteric artery.
  • neuralation - The general term used to describe the early formation of the nervous system. It is often used to describe the early events of differentiation of the central ectoderm region to form the neural plate, then neural groove, then neural tube. The nervous system includes the central nervous system (brain and spinal cord) from the neural tube and the peripheral nervous system (peripheral sensory and sympathetic ganglia) from neural crest. In humans, early neuralation begins in week 3 and continues through week 4.
  • neural crest - region of cells at the edge of the neural plate that migrates throughout the embryo and contributes to many different tissues. In the gastrointestinal tract it contributes mainly the enteric nervous system within the wall of the gut responsible for peristalsis and secretion.
  • peritoneal stomata - the main openings forming the pathways for drainage of intra-peritoneal fluid from the peritoneal cavity into the lymphatic system.
  • pharynx - uppermost end of gastrointestinal and respiratory tract, in the embryo beginning at the buccopharyngeal membrane and forms a major arched cavity within the phrayngeal arches.
  • recanalization - describes the process of a hollow structure becoming solid, then becoming hollow again. For example, this process occurs during GIT, auditory and renal system development.
  • retroperitoneal - (retroperitoneum) is the anatomical space (sometimes a potential space) in the abdominal cavity behind (retro) the peritoneum. Developmentally parts of the GIT become secondarily retroperitoneal (part of duodenum, ascending and descending colon, pancreas)
  • somitogenesis The process of segmentation of the paraxial mesoderm within the trilaminar embryo body to form pairs of somites, or balls of mesoderm. A somite is added either side of the notochord (axial mesoderm) to form a somite pair. The segmentation does not occur in the head region, and begins cranially (head end) and extends caudally (tailward) adding a somite pair at regular time intervals. The process is sequential and therefore used to stage the age of many different species embryos based upon the number visible somite pairs. In humans, the first somite pair appears at day 20 and adds caudally at 1 somite pair/4 hours (mouse 1 pair/90 min) until on average 44 pairs eventually form.
  • splanchnic mesoderm - Gastrointestinal tract (endoderm) associated mesoderm formed by the separation of the lateral plate mesoderm into two separate components by a cavity, the intraembryonic coelom. Splanchnic mesoderm is the embryonic origin of the gastrointestinal tract connective tissue, smooth muscle, blood vessels and contribute to organ development (pancreas, spleen, liver). The intraembryonic coelom will form the three major body cavities including the space surrounding the gut, the peritoneal cavity. The other half of the lateral plate mesoderm (somatic mesoderm) is associated with the ectoderm of the body wall.
  • stomodeum - (stomadeum, stomatodeum) A ventral surface depression on the early embryo head surrounding the buccopharyngeal membrane, which lies at the floor of this depression. This surface depression lies between the maxillary and mandibular components of the first pharyngeal arch.
  • stenosis - abnormal a narrowing of the tube lumen, the abnormality naming is based upon the anatomical location.
  • superior mesenteric artery - main blood supply to the Midgut.
  • viscera - the internal organs in the main cavities of the body, especially those in the abdomen, for example the Template:Intestines.
  • visceral peritoneum - covers the external surfaces of the intestinal tract and organs within the peritoneum. The other component (parietal peritoneum) lines the abdominal and pelvic cavity walls.
  • yolk sac - An extraembryonic membrane which is endoderm origin and covered with extraembryonic mesoderm. Yolk sac lies outside the embryo connected initially by a yolk stalk to the midgut with which it is continuous with. The endodermal lining is continuous with the endoderm of the gastrointestinal tract. The extra-embryonic mesoderm differentiates to form both blood and blood vessels of the vitelline system. In reptiles and birds, the yolk sac has a function associated with nutrition. In mammals the yolk sac acts as a source of primordial germ cells and blood cells. Note that in early development (week 2) a structure called the "primitive yolk sac" forms from hypoblast, this is an entirely different structure.
  • yolk stalk - (vitelline duct, omphalomesenteric duct, Latin, vitellus = yolk of an egg) The endodermal connection between the midgut and the yolk sac. See vitelline duct.
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Additional Information

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Stage 11 to 13

Human embryos digestive tract was initially formed by a narrowing of the yolk sac, and then several derived primordia such as the pharynx, lung, stomach, liver, and dorsal pancreas primordia differentiated during Carnegie stage 12 (21-29 somites) and Carnegie stage 13 (≥ 30 somites).[1]

  • ≥  27 somites - liver bud seen
  • Carnegie stage 13 - dorsal pancreas appeared as definitive buddings
    • ≥  33 somites around dorsal pancreas buddings the small intestine bent
  • ≥  34 somites - stomach is spindle-shaped
  • ≥  35 somites - small intestine rotated around the cranial-caudal axis, begun to form a primitive intestinal loop, which led to umbilical herniation.

Stomach curvature

Recent animal model studies suggest that the main driver of formation of stomach curvature is more about asymmetric growth of the left and right walls of the tube rather than the model of two 90 degree rotations.

  • Stomach curvature is generated by left-right asymmetric gut morphogenesis[2] "Left-right (LR) asymmetry is a fundamental feature of internal anatomy, yet the emergence of morphological asymmetry remains one of the least understood phases of organogenesis. Asymmetric rotation of the intestine is directed by forces outside the gut, but the morphogenetic events that generate anatomical asymmetry in other regions of the digestive tract remain unknown. Here, we show in mouse and Xenopus that the mechanisms that drive the curvature of the stomach are intrinsic to the gut tube itself. The left wall of the primitive stomach expands more than the right wall, as the left epithelium becomes more polarized and undergoes radial rearrangement. These asymmetries exist across several species, and are dependent on LR patterning genes, including Foxj1, Nodal and Pitx2 Our findings have implications for how LR patterning manifests distinct types of morphological asymmetries in different contexts."


  1. <pubmed>26995337</pubmed>
  2. <pubmed>28242610</pubmed>

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Cite this page: Hill, M.A. (2024, April 24) Embryology BGDB Gastrointestinal - Early Embryo. Retrieved from

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