Hindgut and cloaca: the urorectal septum and the pectinate line !

Embryonic structure

The end of the gut opens into the cloaca; a septum splits it into bladder in front and rectum behind. The pectinate line marks where two origins meet.

Updated 2026-11-01

See it in 3D: Rectum · Anal canal · Sigmoid colon · Descending colon · Inferior mesenteric artery · External anal sphincter · Urinary bladder

What it is

The hindgut ends in the cloaca, an endoderm-lined cavity that touches the surface ectoderm at the cloacal membrane. The mesodermal urorectal septum divides it into the urogenital sinus in front and the anorectal canal behind. The upper anal canal is endodermal and the lower part ectodermal; their junction, the pectinate line, separates two different blood supplies, drainages and nerve supplies.

Structure

Cloaca: the terminal dilation of the hindgut, lined by endoderm.
Urorectal septum: a sheet of mesoderm between the allantois and the hindgut.
Cloacal membrane: endoderm and ectoderm in direct contact, with no mesoderm between them.

What it becomes

Distal third of the transverse colon, descending colon and sigmoid colon.
Rectum and upper two-thirds of the anal canal (endoderm).
Lower third of the anal canal (ectoderm of the proctodeum).
Urogenital sinus: lining of the bladder and urethra.

Step by step

The allantois and the hindgut open together into the cloaca.
The cloacal membrane, with no mesoderm between endoderm and ectoderm, closes the cloaca from outside.
Weeks 4 to 7 approx.: the urorectal septum grows between the allantois and the hindgut toward the cloacal membrane.
The cloaca is divided into the urogenital sinus in front and the anorectal canal behind.
The tip of the septum forms the perineal body and splits the membrane into urogenital and anal membranes.
Around the anal membrane the ectoderm forms a depression, the anal pit (proctodeum).
The anal membrane ruptures at the end of the embryonic period and the anal canal opens to the outside.

The pectinate line: what changes

Feature	Above	Below
Origin	Endoderm (hindgut)	Ectoderm (proctodeum)
Epithelium	Simple columnar	Stratified squamous
Artery	Superior rectal (inferior mesenteric)	Inferior rectal (internal pudendal)
Vein	Superior rectal → portal system	Inferior rectal → inferior vena cava
Lymph	Internal iliac nodes	Superficial inguinal nodes
Nerves and pain	Visceral: little pain	Pudendal: sharp pain

Test yourself

Think of the answer, then tap the question to see it.

What divides the cloaca, and what does its tip form?

The urorectal septum; its tip forms the perineal body.

Why are internal haemorrhoids usually painless?

Because they lie above the pectinate line, in endoderm-derived mucosa with visceral innervation.

To which nodes does a tumour of the anal canal below the pectinate line drain?

To the superficial inguinal nodes.

Which urinary linings come from cloacal endoderm?

The lining of the bladder and of the urethra, from the urogenital sinus.

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See it in 3D

The structures of Durgical's 3D anatomy where it is found.

← All of embryology

Educational content on embryonic development; not a guide to prenatal diagnosis or to medicines in pregnancy and no substitute for a health professional's advice. No doses are given.

Sources: Embryology, Rectum and Anal Canal (StatPearls Publishing (NCBI Bookshelf), 2023); Embryology, Gastrointestinal (StatPearls Publishing (NCBI Bookshelf), 2023); Langman's Medical Embryology, 13th ed., ch. 15: Digestive System (Wolters Kluwer, 2015).

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Representative model, for educational purposes only.