The human palatine tonsils (PT) are covered by stratified squamous epithelium that extends into deep and partly branched tonsillar crypts, of which there are about 10 to 30.

[citation needed] The crypts extend through the full thickness of the tonsil reaching almost to its hemicapsule.

[citation needed] The crypt system is not merely a group of invaginations of the tonsillar epithelium but a highly complicated network of canals with special types of epithelium and with various structures surrounding the canals, such as blood and lymphatic vessels and germinal centers.

[citation needed] The largest and deepest of the crypts is the crypta magna located near to the upper pole near the soft palate.

[medical citation needed] These small whitish plugs, termed "tonsilloliths" and sometimes known as "tonsil stones," have a foul smell and can contribute to bad breath; furthermore, they can obstruct the normal flow of pus from the crypts, and may irritate the throat (people with tonsil stones may complain of the feeling that something is stuck in their throat).