Small intestine: villi, crypts, enterocytes, Paneth cells; duodenum vs jejunum vs ileum !

Organ

The small intestine is lined by finger-like villi covered with absorbing cells; each part has a feature that lets you tell it apart.

Updated 2026-11-01

See it in 3D: Duodenum · Jejunum · Ileum

What it is

The small intestine multiplies its surface three times over: circular folds, villi and microvilli. Villi are covered by enterocytes and goblet cells; between them, crypts contain stem cells, Paneth cells and enteroendocrine cells. The duodenum, jejunum and ileum share this plan but differ in landmarks (Brunner glands, fold height, Peyer patches), which is how you identify a biopsy and understand celiac disease and Crohn disease.

Structure

Villus: a core of lamina propria with capillaries and a central lacteal, covered by tall columnar enterocytes with a brush border and scattered goblet cells.
Crypts of Lieberkühn: tubular glands between villi; stem cells near the base renew the lining in a few days.
Paneth cells: at the base of crypts, with bright eosinophilic apical granules of lysozyme and defensins.
Circular folds (plicae circulares): permanent folds of mucosa and submucosa, tallest in the jejunum.

Function

Enterocytes finish digestion with brush-border enzymes (disaccharidases, peptidases) and absorb nutrients.
Lacteals take up fat as chylomicrons into the lymph.
Paneth cells release antimicrobial proteins that shape the gut flora and protect the stem cells.

Duodenum vs jejunum vs ileum vs colon

Feature	Duodenum	Jejunum	Ileum	Colon
Villi	Broad, leaf-like	Tallest, finger-like	Shorter, fewer	None
Circular folds	Begin here	Tallest and most numerous	Fewer, disappear distally	None
Submucosal glands	Brunner glands (alkaline mucus)	None	None	None
Lymphoid tissue	Scattered	Scattered	Peyer patches	Solitary follicles
Goblet cells	Few	More	Many	Most abundant
Main absorption	Iron and calcium	Sugars, amino acids, most nutrients	Vitamin B12, bile salts	Water and electrolytes

Clinical notes

Celiac disease: villous atrophy, crypt hyperplasia and more intraepithelial lymphocytes, mostly in the duodenum; diagnosed with serology and duodenal biopsy.
Crohn disease: transmural inflammation with non-caseating granulomas, most often in the terminal ileum.
Lactase deficiency of the brush border causes lactose intolerance with a normal-looking biopsy.
Giardia duodenalis attaches to duodenal villi and is seen on biopsy as pear-shaped trophozoites.

Test yourself

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

Which glands in the submucosa identify the duodenum?

Brunner (duodenal) glands, which secrete alkaline mucus to neutralize acid chyme from the stomach.

Where are Paneth cells and what do they secrete?

At the base of the intestinal crypts; they secrete antimicrobial proteins such as lysozyme and defensins.

Which segment contains Peyer patches?

The ileum, especially its distal part; they are aggregated lymphoid follicles in the mucosa and submucosa.

What three findings on duodenal biopsy suggest celiac disease?

Villous atrophy, crypt hyperplasia and an increase in intraepithelial lymphocytes.

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See it in 3D

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

Microorganisms

← All of histology

Educational content on normal microscopic structure and its clinical relevance; no substitute for studying slides or for a health professional's advice.

Sources: 23.5 The Small and Large Intestines - Anatomy and Physiology 2e | OpenStax (OpenStax (Rice University), 2022); Small & Large Intestine | SEER Training (National Cancer Institute (SEER Training), 2026); Celiac Disease | MedlinePlus (MedlinePlus (U.S. National Library of Medicine), 2026).

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Representative model, for educational purposes only.