Palatine Tonsils: Anatomy, Histology, and Immune Function

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-09-20

The palatine tonsils are paired aggregates of mucosa-associated lymphoid tissue (MALT) that sit in the tonsillar fossa of the lateral oropharyngeal wall, between the palatoglossal and palatopharyngeal arches. Each tonsil is lined by stratified squamous non-keratinized epithelium that dives into deep branching crypts, and its lymphoid follicles with germinal centers sample antigens from the oral and pharyngeal lumen while draining to the jugular (deep cervical) lymph nodes.

These organs matter because they sit at the front door of the digestive and respiratory tracts. Every breath and every swallow carries microbes, food proteins, and debris across the tonsillar surface. The palatine tonsils are the only major lymphoid organ directly exposed to the external environment, so they function as both a sentinel and a potential point of entry for pathogens [1]. That dual role explains why they are central to mucosal immunity, why they can become infected or chronically inflamed, and why they are studied as a model for antigen sampling across species.

This article is educational and is not a substitute for veterinary diagnosis or treatment.

Where the Palatine Tonsils Sit: Gross Anatomy

Position and the Tonsillar Fossa

The palatine tonsils lie in the tonsillar fossa (also called the tonsillar sinus), a recess in the lateral wall of the oropharynx. Two mucosal folds frame the fossa. The palatoglossal arch runs from the soft palate to the tongue and forms the rostral border. The palatopharyngeal arch runs from the soft palate toward the pharynx and forms the caudal border. The tonsil sits in the pocket between them, which is why the palatine tonsils are described as being "between the arches."

In humans, each palatine tonsil is roughly 2 to 3 cm long in adults, ovoid, and slightly lobulated. Veterinary species vary widely. In the donkey, the tonsil appears as a dome-shaped elevation with a circular opening on the oropharyngeal surface, and the central tonsillar crypt opens on the medial side of the palatopharyngeal fold [2]. In the goat, the palatine tonsil is large and protrudes from a fossa in the lateral wall of the oropharynx, with two to three elongated irregular openings that lead into underlying crypts [3]. In yaks, the palatine tonsils sit in two tonsillar sinuses and are elongated kidney-shaped structures [4].

Relationship to Surrounding Structures

The tonsil is not a free-floating organ. It is anchored to the pharyngeal wall by connective tissue and is partially enclosed by a capsule in several species. In yaks, the palatine tonsils are partially enclosed by a connective tissue capsule with trabeculae extending into the organ, and mucous glands are clearly visible within the encapsulated tissue [4]. In the donkey, the crypt is surrounded by aggregated lymphoid nodules and the cryptal epithelium is infiltrated by lymphocytes [2]. The proximity of the tonsil to the soft palate, tongue base, and pharyngeal muscles means that inflammation can spread locally and cause pain on swallowing.

Blood Supply

The palatine tonsil receives its main arterial supply from the tonsillar branch of the facial artery. The facial artery arises from the external carotid artery and gives off the tonsillar branch as it ascends toward the face. This branch enters the tonsil at its inferior pole and divides into smaller vessels that supply the capsule, septa, and lymphoid tissue. Venous drainage follows a similar path, with veins draining into the pharyngeal plexus and then into the internal jugular vein.

The vascular architecture of the tonsil is specialized for immune function. In the musk shrew, paranodular arterioles enter the lymph nodule and form a coarse capillary plexus within the nodule. Some arterioles reach the dome region and give rise to a fine meshwork of dome subepithelial capillaries. Both nodular and dome capillaries drain into postcapillary venules at the periphery of the nodular or paranodular region, and these venules show oval-shaped indentations corresponding to high endothelial venules [5]. High endothelial venules are the specialized vessels that allow lymphocytes to exit the bloodstream and enter lymphoid tissue.

In humans, CD34 is expressed in capillaries within and below the crypt epithelium, in lymphoid follicles, and in high endothelial venules located para- and interfollicularly. CD146 is expressed on the luminal surface of endothelial cells in the capillaries of the crypt epithelium, while in high endothelial venules it appears on the luminal and lateral surfaces of the cuboidal endothelial cells [6]. These vascular markers help define the microenvironments where immune cells are recruited and where antigen presentation occurs.

Lymphatic Drainage

The palatine tonsils have no afferent lymphatics. This is a key anatomical fact. Lymphatic vessels do not bring lymph into the tonsil. Instead, the tonsil is a source of lymphocytes and antigen-presenting cells that migrate out through efferent lymphatics. The efferent vessels drain to the jugular (deep cervical) lymph nodes, which are the regional nodes for the head and neck. From there, lymph continues into the thoracic duct and eventually returns to the bloodstream.

The absence of afferent lymphatics means that antigens reach the tonsil directly from the surface, not through lymph. This is one reason the tonsil is described as a mucosal sentinel. Antigens must cross the epithelium or be carried across by specialized cells. Once inside, antigen-presenting cells can migrate to the regional lymph nodes and initiate systemic immune responses.

Waldeyer's Ring

The palatine tonsils are part of Waldeyer's ring, a circular arrangement of lymphoid tissue at the entrance to the pharynx. In humans, Waldeyer's ring includes the palatine tonsils, the lingual tonsil at the base of the tongue, the pharyngeal tonsil (adenoid) on the roof of the nasopharynx, and smaller aggregates of lymphoid tissue in the pharyngeal walls. The ring forms a first line of defense where the nasal and oral cavities meet the pharynx.

In veterinary species, the arrangement varies. The lingual tonsil is present in many species and consists of aggregates of lymphoid tissue separated by a median glossoepiglottic ligament that splits the lingual tonsil into right and left halves. Each prominence is covered by non-keratinized epithelium and has a central crypt formed by an invagination of the overlying epithelium. Ducts of adjacent mucous glands empty into the crypt, serving as a flushing mechanism to cleanse the crypt [7]. The palatine tonsils are the largest and most consistently present component of this ring in domestic mammals.

Histology: Epithelium, Crypts, and Lymphoid Tissue

Stratified Squamous Non-Keratinized Epithelium

The surface of the palatine tonsil is covered by stratified squamous non-keratinized epithelium. This type of epithelium has multiple layers of cells, with flattened cells at the surface and more cuboidal or polygonal cells in deeper layers. The cells are living throughout, and the surface is kept moist by saliva and glandular secretions.

The epithelium is not uniform. The surface epithelium overlying the tonsil differs from the crypt epithelium lining the crypts. In humans, the surface and reticular crypt epithelia are differentiated by the expression of multiple cytokeratins, which supports the idea that these epithelia undergo alternate differentiation pathways and possess different functional roles [8]. The crypt epithelium includes reticular areas infiltrated by lymphocytes, and these areas are responsible for antigen sampling [8].

Crypts and Surface Area

The crypts are deep, branching invaginations of the epithelium that extend into the substance of the tonsil. They dramatically increase the surface area available for antigen contact. In the goat, the palatine tonsil has two to three elongated irregular openings that lead to well-developed crypts lined by non-keratinized stratified squamous epithelium [3]. In yaks, each crypt is highly branched and lined with stratified squamous non-keratinized epithelium, and several nonepithelial cells infiltrate between the epithelial cells to form patches of reticular epithelium or lymphoepithelium [4].

The crypt epithelium is a sponge-like structure infiltrated by non-epithelial cells, mostly lymphocytes. It is characterized by the presence of small pores called microcrypts, which are occupied by large microvillus cells and/or lymphocytes. Antigen-presenting Langerhans cells with typical intracytoplasmic Birbeck granules are also found in the crypt epithelium [9]. These features make the crypt epithelium a specialized antigen-sampling surface rather than a simple barrier.

Lymphoid Follicles and Germinal Centers

The lymphoid tissue of the tonsil is organized into follicles. Primary follicles are dense aggregates of small lymphocytes without a germinal center. Secondary follicles have a pale-staining germinal center surrounded by a darker mantle zone. The germinal center is where B lymphocytes proliferate, undergo somatic hypermutation, and differentiate into antibody-secreting plasma cells or memory B cells.

In the donkey, the organized lymphoid nodules are primary and secondary, and the secondary ones have a light germinal center. The interfollicular area has many high endothelial venules and blood capillaries. The endothelial venules are lined by simple cuboidal epithelium and contain lymphocytes [2]. In yaks, lymphoid follicles consist of primary and secondary follicles, and both IgA and IgG antibody-secreting cells are distributed in the interfollicular areas, lymphoid follicles, subepithelial areas, and reticular crypt epithelium [4].

The lymphoid follicles are composed of lymphocytes and two types of non-lymphoid follicular cells: small fibroblast-like cells and large cells morphologically consistent with antigen-bearing follicular dendritic cells or macrophages. The interfollicular areas consist of a dense network of reticular cells and reticular fibers, with many lymphocytes interspersed between the reticular fibers [9].

High Endothelial Venules

High endothelial venules (HEVs) are specialized postcapillary venules with cuboidal endothelial cells. They express adhesion molecules that capture circulating lymphocytes and allow them to migrate into the lymphoid tissue. In the musk shrew, HEVs are found in the periphery of the nodular or paranodular region, and their luminal surfaces show oval-shaped indentations [5]. In humans, HEVs are located para- and interfollicularly and express CD34 and CD146 [6]. The presence of HEVs is a hallmark of organized lymphoid tissue and is essential for continuous lymphocyte recruitment.

Labeled Histology Micrograph Description

A standard hematoxylin and eosin (H&E) stained section of the palatine tonsil shows several distinct zones. At the top of the field, the surface epithelium is stratified squamous non-keratinized, with a basal layer of cuboidal cells and progressively flatter cells toward the surface. Below the surface, a deep crypt invaginates into the tissue. The crypt lumen is narrow and may contain desquamated epithelial cells, lymphocytes, and debris. The crypt epithelium is thinner than the surface epithelium and is heavily infiltrated by small dark lymphocytes, giving it a reticular or spongy appearance. This is the lymphoepithelium.

Deeper in the section, lymphoid follicles are visible. A secondary follicle has a pale center (the germinal center) with larger, less condensed nuclei and a darker rim (the mantle zone) of small, densely packed lymphocytes. Between follicles, the interfollicular area contains a mix of lymphocytes, plasma cells, and reticular cells. Small blood vessels and high endothelial venules are scattered through the interfollicular and paranodular regions. A connective tissue capsule may be visible at the base of the section, with trabeculae extending inward. In species with mucous glands, such as yaks and goats, glandular acini may be seen near the capsule or in the submucosa [3][4].

Immune Function: Antigen Sampling and Response

The Crypt Epithelium as an Antigen Sampling Surface

The crypt epithelium is the primary site of antigen sampling. Its structure is adapted for this role. The epithelium is thin, infiltrated by lymphocytes, and contains microcrypts and pores that allow antigens to reach immune cells. In pigs, the crypt epithelium is the first barrier of the tonsil, and understanding the early changes in leucocyte subpopulations in response to infection is critical for clarifying disease pathogenesis and for developing mucosal vaccines [10].

In a study of pigs infected with Streptococcus suis type 2, researchers used monoclonal antibodies against leucocyte markers CD3, CD4, CD8, gamma-delta T cell receptor, lambda-immunoglobulin light-chain, myeloid cells, and MHC class II. They found an increase in lambda-immunoglobulin light-chain positive cells (a B cell subset) in crypts of infected animals from 18 hours after infection onward, with a significant increase at 18 and 48 hours. The number of CD4 and CD8 cells was greater from 18 hours onward, with a significant increase at 24 and 72 hours post-infection [10]. These findings show that the crypt epithelium rapidly recruits and organizes immune cells after exposure to a pathogen.

Antigen Transport and Presentation

Antigens that enter the crypts are taken up by macrophages and other antigen-presenting cells. In a study using horseradish peroxidase (HRP) dropped into the crypts, HRP entered through the microcrypts, was phagocytosed by macrophages, gathered mostly around the vessels, and emigrated to the regional lymph nodes. Anti-HRP antibody-producing cells were observed not only in the tonsil but also in the regional lymph node [1]. This demonstrates that the tonsil does not act in isolation. It samples antigen locally and then communicates with the regional lymph nodes to mount a broader immune response.

Langerhans cells in the crypt epithelium are also involved in antigen presentation. These cells have typical intracytoplasmic Birbeck granules and are positioned to capture antigens and migrate to T cell zones [9]. The presence of these specialized cells confirms that the tonsil is equipped for both innate and adaptive immune responses.

B Cell and T Cell Responses

The tonsil supports both B cell and T cell responses. B cells are concentrated in follicles and germinal centers, where they undergo affinity maturation and class switching. T cells are found in the interfollicular areas and in the crypt epithelium. In yaks, IgA and IgG antibody-secreting cells are distributed in the interfollicular areas, lymphoid follicles, subepithelial areas, and reticular crypt epithelium [4]. The presence of IgA-secreting cells is particularly important for mucosal immunity, because IgA is the main antibody class in secretions and helps neutralize pathogens at mucosal surfaces.

In Bactrian camels, IgE-secreting cells have been identified in the palatine tonsils. IgE is associated with allergic responses and defense against parasites. The distribution of IgE-secreting cells in the tonsil suggests that the tonsil may play a role in local allergic responses as well as antimicrobial immunity [11].

The Epithelial Barrier and Tight Junctions

The epithelium of the tonsil is not a passive barrier. It actively regulates what crosses it. Tight junctions are protein complexes that seal the spaces between epithelial cells and control paracellular permeability. In human palatine tonsils, occludin, ZO-1, JAM-1, and claudin-1, -3, -4, -7, -8, and -14 mRNAs are detected in tonsillar hypertrophy. Occludin and claudin-14 are expressed in the uppermost layer of the surface epithelium, while ZO-1, JAM-1, and claudin-1, -4, and -7 are found throughout the epithelium. In the crypt epithelium, claudin-4 is preferentially expressed in the upper layers. In freeze-fracture replicas, short fragments of continuous tight junction strands are observed but never form networks [12].

In recurrent tonsillitis, the tracer leaks from surface regions where occludin and claudin-4 disappear. Occludin, ZO-1, JAM-1, and claudin-1, -3, -4, and -14 mRNAs are decreased in recurrent tonsillitis compared with tonsillar hypertrophy [12]. These findings suggest that the crypt epithelium possesses an epithelial barrier different from that of the surface epithelium, and that disruption of this barrier may contribute to recurrent infection.

Fibronectin and Pathogen Adhesion

Fibronectin is an extracellular matrix protein that can act as a receptor for bacterial adhesion. In the palatine tonsil, fibronectin is found in the basal layers of surface epithelium, subepithelial connective tissue, and interfollicular areas. In children from rheumatic families, fibronectin immunoreactivity is significantly increased in subepithelial connective tissue areas, and there are more than one apparent crypt epithelial disruption compared to normal children [13]. Fibronectin is the major receptor on the surface of the human palatine tonsil for group A streptococci, which are the bacteria that trigger rheumatic fever. This makes fibronectin a marker for rheumatic susceptibility and a factor in the pathogenesis of post-streptococcal disease [13].

Comparative Anatomy Across Species

Summary Table: Palatine Tonsils in Domestic Species

Dogs and Cats

In the dog, the palatine tonsil is a compact structure that sits in a sinus (the tonsillar fossa) on the lateral wall of the oropharynx. It is less protruding than the tonsils of ruminants and pigs. The crypt system is relatively simple, often with a single main crypt or a few shallow branches. In the cat, the palatine tonsil is smaller and less prominent. The general histology is similar to other species, with stratified squamous non-keratinized epithelium, crypts, and lymphoid follicles.

Pigs

The pig palatine tonsil is of particular interest because of its role in Streptococcus suis infection. S. suis is a common cause of meningitis, septicemia, and arthritis in pigs, and the tonsils are a portal of entry and a site of multiplication and persistence [10]. The crypt epithelium is the first barrier, and it responds rapidly to infection by recruiting B cells, CD4 T cells, and CD8 T cells [10]. This makes the pig tonsil a valuable model for studying mucosal immunity and vaccine development.

Horses and Donkeys

In the donkey, the palatine tonsil is dome-shaped with a slight elevation and a circular opening on the surface of the oropharynx. The central tonsillar crypt appears on the medial side of the palatopharyngeal folds and the floor of the oropharynx. The external surface has mucosal folds and grooves directed to drainage at the tonsillar opening, and the crypt opening is crescentic or irregular oval. The outer surface is covered by stratified squamous epithelium and modified to be reticular epithelium invaded by lymphocytes in the crypt, called lymphoepithelium. The crypt has aggregated lymphoid nodules, and the cryptal epithelium is surrounded by diffuse lymphocytes and Hassall's corpuscle-like structures. The lymphocytes infiltrate different layers of the cryptal epithelium and transform into reticular or lymphoepithelium. The organized lymphoid nodules are primary and secondary, and the secondary ones have a light germinal center [2].

Ruminants

Ruminants have prominent palatine tonsils. In the goat, the palatine tonsil is large and protrudes from a fossa in the lateral wall of the oropharynx. It has two to three elongated irregular openings that lead to well-developed crypts lined by non-keratinized stratified squamous epithelium [3]. The soft palate of the goat is covered by non-keratinized stratified squamous epithelium, and the lamina propria and submucosa contain diffuse and nodular lymphatic tissue, striated muscle fibers, and a large number of mucous and serous palatine glands [3].

In yaks, the palatine tonsils are elongated kidney-shaped structures found in two tonsillar sinuses. They have external and internal crypts, and each crypt is highly branched and lined with stratified squamous non-keratinized epithelium. The tonsils are partially enclosed by a connective tissue capsule with trabeculae, and mucous glands are clearly visible. In newborn yaks, lymphoid follicles are not observed. In older yaks, lymphoid follicles consist of primary and secondary follicles, and both IgA and IgG antibody-secreting cells are distributed throughout the tonsil [4].

Camels

In Bactrian camels, the palatine tonsils have been studied for the distribution of IgE-secreting cells. IgE-secreting cells are mainly found in the palatine tonsils, suggesting a role in local allergic responses and defense against parasites [11]. This is an area of active research because camels live in sandy environments and may have unique mucosal immune adaptations.

Peccaries

The collared peccary has two ovoid-shaped tonsils in the soft palate, with several crypts on the surface. The epithelium is highly infiltrated by lymphocytes, and tonsilloliths (calcified deposits) are frequently observed within the crypts [14]. The general organization of the peccary palate is similar to other species, but in its oropharynx, only the soft palate tonsil is present [14].

Clinical Relevance, Limitations and Common Mistakes

The palatine tonsils are clinically relevant because they are a common site of infection and inflammation. Tonsillitis can be caused by bacteria, viruses, or both. In pigs, Streptococcus suis infection of the tonsils can lead to meningitis, septicemia, and arthritis [10]. In humans, group A streptococcal tonsillopharyngitis can trigger rheumatic fever and rheumatic heart disease, and fibronectin in the tonsil is a marker for rheumatic susceptibility [13].

The tonsils are also a site of origin for some cancers. In humans, the tonsillar crypts are the site of origin of most HPV-induced oropharyngeal squamous cell carcinomas. ALDH1A1 is uniquely expressed in a subset of suprabasal tonsillar crypt epithelium, and NGFR-expressing cells are considered the resident stem/progenitor cells in tonsillar crypts. Both NGFR and ALDH1A1 are lost in HPV-positive and HPV-negative tumors, while LGR5 expression is induced in the same tumors [15]. This research helps explain how tonsillar crypt cells can transform into cancer cells.

Blood supply to the tonsil is clinically important because of the risk of hemorrhage during surgery. The tonsillar branch of the facial artery is the main supply, but anomalous structures of the internal carotid artery can increase the risk of intra- and postoperative hemorrhage. Inflammatory changes in the tonsil and peritonsillar region can also increase bleeding risk [16]. This is why imaging and careful preoperative assessment are important before any surgical intervention on the pharynx.

Common mistakes students make when studying the palatine tonsils include confusing them with the lingual tonsil, forgetting that they have no afferent lymphatics, and assuming that all species have the same crypt pattern. The lingual tonsil is at the base of the tongue and has its own crypts and mucous gland ducts [7]. The palatine tonsils are in the oropharyngeal wall between the arches. The absence of afferent lymphatics is a defining feature that distinguishes the tonsil from a lymph node. Species differences in crypt depth, location, and prominence are substantial, as shown in the comparative table.

Another common mistake is to think of the tonsil as a simple barrier. The crypt epithelium is a specialized antigen-sampling surface with tight junctions that are different from those of the surface epithelium [12]. Disruption of these tight junctions is associated with recurrent tonsillitis [12]. The tonsil is an active immune organ, not a passive filter.

Individual cases require veterinary assessment. The information here is educational and cannot replace a physical examination, history, and diagnostic testing for a specific animal.

Quick Review

1. The palatine tonsils are paired lymphoid organs in the tonsillar fossa between the palatoglossal and palatopharyngeal arches.
2. They are lined by stratified squamous non-keratinized epithelium with deep branching crypts that increase surface area for antigen sampling.
3. Lymphoid follicles with germinal centers contain B cells, and interfollicular areas contain T cells and high endothelial venules.
4. The palatine tonsils are part of Waldeyer's ring, have no afferent lymphatics, and drain to the jugular (deep cervical) lymph nodes.
5. Blood supply is mainly from the tonsillar branch of the facial artery.
6. The crypt epithelium is a lymphoepithelium with microcrypts, Langerhans cells, and tight junctions that regulate permeability.
7. Species differences are significant: dogs have a compact tonsil in a sinus, cats have a small tonsil, pigs have crypts that respond rapidly to infection, horses and donkeys have a dome-shaped tonsil with lymphoepithelium, and ruminants have large, prominent tonsils with highly branched crypts.

Frequently Asked Questions

What are the palatine tonsils?

The palatine tonsils are paired aggregates of lymphoid tissue located in the tonsillar fossa of the lateral oropharyngeal wall, between the palatoglossal and palatopharyngeal arches. They are part of Waldeyer's ring and function in mucosal immune defense.

Do the palatine tonsils have afferent lymphatics?

No. The palatine tonsils have no afferent lymphatics. They receive antigens directly from the surface and send efferent lymph to the jugular (deep cervical) lymph nodes.

What type of epithelium covers the palatine tonsils?

The palatine tonsils are covered by stratified squamous non-keratinized epithelium. The crypt epithelium is thinner, infiltrated by lymphocytes, and forms a reticular or lymphoepithelium specialized for antigen sampling.

What is the blood supply to the palatine tonsil?

The main blood supply is the tonsillar branch of the facial artery. Venous drainage goes to the pharyngeal plexus and then to the internal jugular vein.

How do palatine tonsils differ between dogs and ruminants?

Dogs have a compact tonsil in a sinus with simple crypts. Ruminants such as goats and yaks have large, protruding tonsils with well-developed, highly branched crypts and prominent lymphoid tissue.

What immune cells are found in the palatine tonsils?

The palatine tonsils contain B cells in follicles and germinal centers, T cells in interfollicular areas and crypt epithelium, macrophages, Langerhans cells, and antibody-secreting cells that produce IgA, IgG, and IgE depending on the species.

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