Gastrointestinal Tract - Intestine Development

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midgut herniation

The part of the gastrointestinal tract (GIT) lying between the stomach and anus, is described as the intestines or bowel. 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). Initially development concerns the midgut region, connected to the yolk sac, and the hindgut region, ending at the cloacal membrane. This is followed by two mechanical processes of elongation and rotation. Elongation, growth in length, leaves the midgut "herniated" at the umbilicus and external to the abdomen. Rotation, around a mesentery axis, establishes the anatomical position of the large intestine within the peritoneal space.

Migration of neural crest cells into the wall establishes the enteric nervous system, which has a role in peristalsis and secretion. Prenatally, secretions also accumulate in this region and are the first postnatal bowel movement, the meconium.

The small intestine grows in length rapidly in the last trimester, at birth it is about half the eventual adult length (More? Small Intestine Length). Like most of the gut, this region is not "functional" until after birth, when development continues by populating the large intestine with commensal bacteria and the establishment of the immune structure in the wall.

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GIT Histology Links: Upper GIT | Salivary Gland | Smooth Muscle Histology | Liver | Gall Bladder | Pancreas | Colon | Histology Stains | Histology | GIT Development
Historic Embryology - Gastrointestinal Tract  
1878 Alimentary Canal | 1882 The Organs of the Inner Germ-Layer The Alimentary Tube with its Appended Organs | 1902 The Organs of Digestion | 1903 Submaxillary Gland | 1906 Liver | 1907 Development of the Digestive System | 1907 Atlas | 1907 23 Somite Embryo | 1908 Liver and Vascular | 1910 Mucous membrane Oesophagus to Small Intestine | 1910 Large intestine and Vermiform process | 1912 Digestive Tract | 1912 Stomach | 1914 Digestive Tract | 1914 Intestines | 1914 Rectum | 1915 Pharynx | 1915 Intestinal Rotation | 1917 Entodermal Canal | 1918 Anatomy | 1921 Alimentary Tube | 1932 Gall Bladder | 2008 Liver | 2016 GIT Notes | Historic Disclaimer
Human Embryo: 1908 13-14 Somite Embryo | 1921 Liver Suspensory Ligament | 1926 22 Somite Embryo | 1907 23 Somite Embryo | 1937 25 Somite Embryo | 1914 27 Somite Embryo | 1914 Week 7 Embryo
Animal Development: 1913 Chicken | 1951 Frog
Historic Embryology: 1912 Small Intestine | 1912 large Intestine | 1915 Intestinal Rotation

Some Recent Findings

Model for cloacal septation[1]
  • Digestive Tract in Human Embryos Between Carnegie Stages 11 and 13[2] "We selected 37 human embryos at Carnegie Stage (CS) 11-CS13 (28-33 days after fertilization) and three-dimensionally analyzed the morphology and positioning of the digestive tract and derived primordia in all samples, using images reconstructed from histological serial sections. The 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 CS12 (21-29 somites) and CS13 (≥ 30 somites). The differentiation of four pairs of pharyngeal pouches was complete in all CS13 embryos. The respiratory primordium was recognized in ≥ 26-somite embryos and it flattened and then branched at CS13. The trachea formed and then elongated in ≥ 35-somite embryos. The stomach adopted a spindle shape in all ≥ 34-somite embryos, and the liver bud was recognized in ≥ 27-somite embryos. The dorsal pancreas appeared as definitive buddings in all but three CS13 embryos, and around these buddings, the small intestine bent in ≥ 33-somite embryos. In ≥ 35-somite embryos, the small intestine rotated around the cranial-caudal axis and had begun to form a primitive intestinal loop, which led to umbilical herniation."
  • Review - How to make an intestine[3] With the high prevalence of gastrointestinal disorders, there is great interest in establishing in vitro models of human intestinal disease and in developing drug-screening platforms that more accurately represent the complex physiology of the intestine. We will review how recent advances in developmental and stem cell biology have made it possible to generate complex, three-dimensional, human intestinal tissues in vitro through directed differentiation of human pluripotent stem cells.
  • Bmp7 functions via a polarity mechanism to promote cloacal septation[1] "During normal development in human and other placental mammals, the embryonic cloacal cavity separates along the axial longitudinal plane to give rise to the urethral system, ventrally, and the rectum, dorsally. Defects in cloacal development are very common and present clinically as a rectourethral fistula in about 1 in 5,000 live human births. Yet, the cellular mechanisms of cloacal septation remain poorly understood. ...Our results strongly indicate that Bmp7/JNK signaling regulates remodeling of the cloacal endoderm resulting in a topological separation of the urinary and digestive systems. Our study points to the importance of Bmp and JNK signaling in cloacal development and rectourethral malformations."
  • Fgf9 signaling regulates small intestinal elongation and mesenchymal development [4] "Short bowel syndrome is an acquired condition in which the length of the small intestine is insufficient to perform its normal absorptive function. ...These data suggest a model in which epithelial-derived Fgf9 stimulates intestinal mesenchymal stem cells (iMSCs) that in turn regulate underlying mesenchymal fibroblast proliferation and differentiation at least in part through inhibition of Tgfbeta signaling in the mesenchyme."
More recent papers
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This table shows an automated computer PubMed search using the listed sub-heading term.

  • Therefore the list of references do not reflect any editorial selection of material based on content or relevance.
  • References appear in this list based upon the date of the actual page viewing.

References listed on the rest of the content page and the associated discussion page (listed under the publication year sub-headings) do include some editorial selection based upon both relevance and availability.

Links: References | Discussion Page | Pubmed Most Recent | Journal Searches

Search term: Intestine Embryology

Gezahen Negusse Ayane, Mikel Walsh, Jemal Shifa, Kadimo Khutsafalo Right congenital diaphragmatic hernia associated with abnormality of the liver in adult. Pan Afr Med J: 2017, 28;70 PubMed 29255540

B U Metzler-Zebeli, E Magowan, M Hollmann, M E E Ball, A Molnár, K Witter, R Ertl, R J Hawken, P G Lawlor, N E O'Connell, J Aschenbach, Q Zebeli Differences in intestinal size, structure, and function contributing to feed efficiency in broiler chickens reared at geographically distant locations. Poult. Sci.: 2017; PubMed 29253222

Spyridon Pagkratis, Sara Kryeziu, Miranda Lin, Samah Hoque, Juan Carlos Bucobo, Jonathan M Buscaglia, Georgios V Georgakis, Aaron R Sasson, Joseph Kim Case report of intestinal non-rotation, heterotaxy, and polysplenia in a patient with pancreatic cancer. Medicine (Baltimore): 2017, 96(49);e8599 PubMed 29245220

S A Pereira, G T Jerônimo, N C Marchiori, H M Oliveira, G F A Jesus, E C Schmidt, Z L Bouzon, F N Vieira, M L Martins, J L P Mouriño Tadpoles fed supplemented diet with probiotic bacterium isolated from the intestinal tract of bullfrog Lithobates catesbeianus: Haematology, cell activity and electron microscopy. Microb. Pathog.: 2017; PubMed 29174701

Fuman She, Shengwen Dong, Bibo Yuan, Xiaoli Gao Diagnosis of fetal megacystis with chromosomal abnormality by 2D prenatal ultrasound: A case report. Medicine (Baltimore): 2017, 96(46);e8589 PubMed 29145274

Adult Small Intestine

Duodenum cartoon.jpg Jejunum and ileum cartoon.jpg
Duodenum Jejunum and ileum
  • Duodenum (adult 25 cm length)
  • Jejunum (adult 1.4 m length)
  • Ileum (adult 3.5 m length)

The adult ileum contains specialised aggregated lymphoid nodules known as Peyer's patches.

Intestine histology 001.jpg Peyer's patch 01.jpg
Adult jejunum histology Adult ileum Peyer's patches

See small intestine or bowel length (see also Fetal Intestine Length and Small Intestine Length)

Large intestine or bowel

  • Cecum (caecum)
    • Vermiform appendix ("appendix", adult 2 to 20 cm length)
  • Colon
    • Ascending colon (adult 25 cm length)
    • Transverse colon
    • Descending colon
    • Sigmoid colon

Intestinal Functions

Small Intestine

  • absorption of nutrients and minerals found in food
  • Duodenum -principal site for iron absorption


  • connects the ileum with the ascending colon
  • separated by the ileocecal valve (ICV, Bauhin's valve)
  • connected to the vermiform appendix ("appendix")


  • absorbs fluid, water and salts, from solid wastes
  • site of commensal bacteria (flora) fermentation of unabsorbed material

Embryonic Development

Week 4


Colour code:

  • Foregut - oropharyngeal membrane, oesophagus, pharynx (dark salmon - Foregut, oropharyngeal membrane, oesophagus, pharynx)
  • Trachea and Lung Buds (dark blue - Trachea and Lung Buds)
  • Mesonephros (yellow - mesonephros)
  • Mesonephric Ducts (light blue - mesonephric ducts)
  • Hindgut and Cloaca (brown - hindgut and cloaca)
 ‎‎GIT Stage 13
Page | Play

Week 7

Small intestine secondary loops week 7 to 8

Human embryo small intestine secondary loops (week 7 to 8).[5]

Week 8

 ‎‎GIT Stage 22
Page | Play

Stage 22 image 088.jpg Stage 22 image 089.jpg

Late embryonic small intestine commencing at the duodenum, continuing as ventrally herniated and returning to join the colon.

Small intestine tertiary loops week 8

Small intestine tertiary loops week 8.[5]

Links: Carnegie stage 22 | Week 8


A recent 3 dimensional study[5] has suggested a modified “en-bloc rotation” of the small intestine, compared the the earlier simplified description of 270 degree rotation (below).

Human intestine “en-bloc rotation” model.jpg

Human intestine “en-bloc rotation” model.[5]

"If one insists on using the term rotation for this movement, it would be largely around a craniocaudal axis (in the transverse plane) rather than a dorsoventral axis (frontal plane). In view of the brief time window and orientation of the apparent rotational axis, we conclude that the distal ileum and cecum “slide” rather than “rotate” as from the umbilical orifice to the lower-right abdominal cavity."

Normal intestinal rotation cartoon.jpg

Normal intestinal rotation[6]

Fetal Intestine Length

Fetal small Intestine length growth graph.jpg Fetal large Intestine length growth graph.jpg
Fetal small Intestine length growth Fetal Large Intestine length growth

Data from [7][8]

Small Intestine Length

Small intestine growth in length is initially linear (first half pregnancy to 32 cm CRL), followed by rapid growth in the last 15 weeks doubling the overall length. Growth continues postnatally but after 1 year slows again to a linear increase to adulthood.[9]

Age (weeks gestational age) Average Length (cm)
20 125
30 200
term 275
1 year postnatal 380
5 years 450
10 years 500
20 years 575

Table data based upon 8 published reports of necropsy measurement of 1010 guts.[9]


The appendix (vermiform appendix, vermix) is a finger-like diverticulum located anatomically at the cecum, the junction between the small and large intestines (colon). The length (2.5-13 cm) is longer in both infants and children and also has more abundant lymphatic tissue in early life. The wall structure is similar to the small intestine (though with no villi), nor plicae circularis. Its immune function is associated with the many lymph nodules surrounding the lumen that extend from the mucosa into the submucosa. It has also been suggested as a repository for beneficial intestinal microflora. See also the review comparing the appendix in different species.[10]

There appears to be a developmental anatomical differences in the fetal position of the appendix in males and females.[11] In the fetus, lymphocyte aggregates first appear in this region during the second trimester, week 15 (GA week 17).[12]

Historically, Berengario da Carpi (1460-c.1530) in Commentaria cum amplissimis additionibus super Anatomia Mundini (1521) was the first to describe the human appendix.

Links: Immune System Development | Lecture - Lymphatic Structure and Organs


Anatomically the distal third of the transverse colon and the splenic flexure, the descending colon, sigmoid colon and rectum. The developmental timing of the anus and rectum formation[13] in human embryos of the Carnegie Collection has been previously carried out (1974). A more recent study[14] has also been made of the Kyoto Collection embryos.

There has been some recent controversy over the "anal membrane" formation.

A recent study hindgut and anorectum development in human embryos shows that Wnt5a is active in this region prior to anus formation, when it is down-regulated.[15]

Other studies - PMID 19496155 PMID 10504783 PMID 9562679 PMID 9243909 PMID 21708335 (rat)

Intestinal Motility

The enteric nervous system neural crest-derived neurons interacts with the circular and longitudinal smooth muscle layers and the interstitial cells of Cajal to generate motility. The developmental timing data shown below is from a recent review.[16]

Neural Crest

week 5 - migrating neural crest cells reach the midgut

week 7 - neural crest cells have colonized the entire gut

  • colonization occurs in a rostro-caudal sequence

Myenteric plexus (Auerbach's plexus, named after Leopold Auerbach (1828–1897) a German anatomist and neuropathologist.)

  • is first formed plexus
  • lies between the outer longitudinal and inner circular layers of muscularis externa
  • provides motor innervation to both layers
  • secretomotor innervation to the mucosa
  • has both parasympathetic and sympathetic input

Submucosal Plexus (Meissner's plexus, named after Georg Meissner (1829–1905) a German anatomist and physiologist.)

  • forms 2-3 days after the myenteric plexus
  • formed by cells migrating from the myenteric plexus
  • innervates smooth muscle of the muscularis mucosae
  • has only parasympathetic fibers

Smooth Muscle

week 8 - esophagus circular muscle

week 11 - hindgut circular muscle

week 14 - hindgut concentric muscularis mucosae, circular muscle, and longitudinal muscle

Interstitial Cells of Cajal

Interstitial cells of Cajal (ICC) are electrical pacemaker cells within the gastrointestinal tract smooth muscle. They create the basal (slow waves) rhythm required for contraction and peristalsis. They are mesodermal in origin.

weeks 7-9 - cells initially appear

week 11 - distinct clusters

week 12-14 - clustered around myenteric ganglia along the entire gut

Links: Neural Crest Development


Abnormality Links: Gastrointestinal Tract - Abnormalities | Intestine Development | Gastrointestinal Tract
Links: Gastrointestinal Tract - Abnormalities | Image - Small intestine duplication

Appendix Duplication

Appendix duplication is an extremely rare congenital anomaly (0.004% to 0.009% of appendectomy specimens) first classified according to their anatomic location by Cave in 1936[17] and a later modified by Wallbridge in 1963[18], subsequently two more types of appendix abnormalities have been identified.[19][20]

Modified Cave-Wallbridge Classification (table from[21])

Classification of types
of appendix duplication
A Single cecum with various degrees of incomplete duplication
B1 (bird type) Two appendixes symmetrically placed on either side of the ileocecal valve
B2 (tenia coli type) ne appendix arises from the cecum at the usual site, and the second

appendix branches from the cecum along the lines of the tenia at various distances from the first

B3 One appendix arises from the usual site, and the second appendix arises from

the hepatic flexura

B4 One appendix arises from the usual site, and the second appendix arises from

the splenic flexura

C Double cecum, each with an appendix
Horseshoe appendix One appendix has two openings into a common cecum
Triple appendix One appendix arises from the cecum at the usual site, and two additional appendixes arise from the colon

Short Bowel Syndrome

Short bowel syndrome (SBS) results typically due to developmental abnormalities, extensive intestinal resection during the neonatal period, or necrotising enterolitis.[22]

  • reduces gut function for digestion and absorption of nutrients (intestinal failure).

Links: PubMed Health | Better Health

Molecular Factors

  • Cdx (Caudal-type homeobox) group of ParaHox genes (mouse Cdx1, Cdx2 and Cdx4)[23]
  • FGF9


  1. 1.0 1.1 Kun Xu, Xinyu Wu, Ellen Shapiro, Honging Huang, Lixia Zhang, Duane Hickling, Yan Deng, Peng Lee, Juan Li, Herbert Lepor, Irina Grishina Bmp7 functions via a polarity mechanism to promote cloacal septation. PLoS ONE: 2012, 7(1);e29372 PubMed 22253716
  2. Saki Ueno, Shigehito Yamada, Chigako Uwabe, Jörg Männer, Naoto Shiraki, Tetsuya Takakuwa The Digestive Tract and Derived Primordia Differentiate by Following a Precise Timeline in Human Embryos Between Carnegie Stages 11 and 13. Anat Rec (Hoboken): 2016, 299(4);439-449 PubMed 26995337
  3. James M Wells, Jason R Spence How to make an intestine. Development: 2014, 141(4);752-60 PubMed 24496613 | Development
  4. Michael J Geske, Xiuqin Zhang, Khushbu K Patel, David M Ornitz, Thaddeus S Stappenbeck Fgf9 signaling regulates small intestinal elongation and mesenchymal development. Development: 2008, 135(17);2959-68 PubMed 18653563
  5. 5.0 5.1 5.2 5.3 Jelly Hm Soffers, Jill Pjm Hikspoors, Hayelom K Mekonen, S Eleonore Koehler, Wouter H Lamers The growth pattern of the human intestine and its mesentery. BMC Dev. Biol.: 2015, 15(1);31 PubMed 26297675
  6. Vicki Martin, Charles Shaw-Smith Review of genetic factors in intestinal malrotation. Pediatr. Surg. Int.: 2010, 26(8);769-81 PubMed 20549505 | PMC2908440
  7. J FitzSimmons, A Chinn, T H Shepard Normal length of the human fetal gastrointestinal tract. Pediatr Pathol: 1988, 8(6);633-41 PubMed 3244599
  8. John G Archie, Julianne S Collins, Robert Roger Lebel Quantitative standards for fetal and neonatal autopsy. Am. J. Clin. Pathol.: 2006, 126(2);256-65 PubMed 16891202
  9. 9.0 9.1 L T Weaver, S Austin, T J Cole Small intestinal length: a factor essential for gut adaptation. Gut: 1991, 32(11);1321-3 PubMed 1752463 | PMC1379160 | Gut.
  10. R E Fisher The primate appendix: a reassessment. Anat. Rec.: 2000, 261(6);228-36 PubMed 11135184
  11. M A Malas, A Gökçimen, O Sulak Growing of caecum and vermiform appendix during the fetal period. Fetal. Diagn. Ther.: 2001, 16(3);173-7 PubMed 11316934
  12. M Ali Malas, O Sulak, A Gökçimen, A Sari Development of the vermiform appendix during the fetal period. Surg Radiol Anat: 2004, 26(3);202-7 PubMed 15173960
  13. de Vries PA. and Friedland GW. The staged sequential development of the anus and rectum in human embryos and fetuses. (1974) J. Pediatr. Surg., 9(5): 755-69 PMID 4424274
  14. Ryozo Hashimoto Development of the human tail bud and splanchnic mesenchyme. Congenit Anom (Kyoto): 2013, 53(1);27-33 PubMed 23480355
  15. Fei Fei Li, Tao Zhang, Yu Zuo Bai, Zheng Wei Yuan, Wei Lin Wang Spatiotemporal expression of Wnt5a during the development of the hindgut and anorectum in human embryos. Int J Colorectal Dis: 2011, 26(8);983-8 PubMed 21431850
  16. Alan J Burns, Rachael R Roberts, Joel C Bornstein, Heather M Young Development of the enteric nervous system and its role in intestinal motility during fetal and early postnatal stages. Semin. Pediatr. Surg.: 2009, 18(4);196-205 PubMed 19782301
  17. A J Cave Appendix Vermiformis Duplex. J. Anat.: 1936, 70(Pt 2);283-92 PubMed 17104589
  18. P H WALLBRIDGE Double appendix. Br J Surg: 1962, 50;346-7 PubMed 13998581
  19. T W Mesko, R Lugo, T Breitholtz Horseshoe anomaly of the appendix: a previously undescribed entity. Surgery: 1989, 106(3);563-6 PubMed 2772830
  20. L F Tinckler Triple appendix vermiformis--a unique case. Br J Surg: 1968, 55(1);79-81 PubMed 5635427
  21. Emel Canbay, Emel Akman Appendix perforation in appendix duplication in a man: a case report. J Med Case Rep: 2011, 5;162 PubMed 21513538 | J Medical Case Reports | PDF
  22. G Davì, A Pinto, M G Palumbo, V Gallo, A Mazza, A Strano Dipyridamole and aspirin in arteriosclerosis obliterans of the lower limbs. Adv. Prostaglandin Thromboxane Leukot. Res.: 1985, 13;271-5 PubMed 3159212
  23. Felix Beck, Emma J Stringer The role of Cdx genes in the gut and in axial development. Biochem. Soc. Trans.: 2010, 38(2);353-7 PubMed 20298182


James M Wells, Jason R Spence How to make an intestine. Development: 2014, 141(4);752-60 PubMed 24496613

Taeko K Noah, Bridgitte Donahue, Noah F Shroyer Intestinal development and differentiation. Exp. Cell Res.: 2011, 317(19);2702-10 PubMed 21978911

Alan J Burns, Rachael R Roberts, Joel C Bornstein, Heather M Young Development of the enteric nervous system and its role in intestinal motility during fetal and early postnatal stages. Semin. Pediatr. Surg.: 2009, 18(4);196-205 PubMed 19782301


Jelly Hm Soffers, Jill Pjm Hikspoors, Hayelom K Mekonen, S Eleonore Koehler, Wouter H Lamers The growth pattern of the human intestine and its mesentery. BMC Dev. Biol.: 2015, 15(1);31 PubMed 26297675

Yui Ueda, Shigehito Yamada, Chigako Uwabe, Katsumi Kose, Tetsuya Takakuwa Intestinal rotation and physiological umbilical herniation during the embryonic period. Anat Rec (Hoboken): 2015; PubMed 26599074

Tae-Hee Kim, Byeong-Moo Kim, Junhao Mao, Sheldon Rowan, Ramesh A Shivdasani Endodermal Hedgehog signals modulate Notch pathway activity in the developing digestive tract mesenchyme. Development: 2011, 138(15);3225-33 PubMed 21750033

Won Kyu Kim, Hyun Kim, Dae Ho Ahn, Myoung Hee Kim, Hyoung Woo Park Timetable for intestinal rotation in staged human embryos and fetuses. Birth Defects Res. Part A Clin. Mol. Teratol.: 2003, 67(11);941-5 PubMed 14745932

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Pages where the terms "Historic Textbook" and "Historic Embryology" appear on this site, and sections within pages where this disclaimer appears, indicate that the content and scientific understanding are specific to the time of publication. This means that while some scientific descriptions are still accurate, the terminology and interpretation of the developmental mechanisms reflect the understanding at the time of original publication and those of the preceding periods, these terms and interpretations may not reflect our current scientific understanding.     (More? Embryology History | Historic Embryology Papers)

Frazer JE. and Robbins RH. On the factors concerned in causing rotation of the intestine in man. (1915) J Anat Physiol. 50(1): 75-110. PMID 17233053

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