What to Do About Cryptic Tonsils

Tonsillar crypts are pockets or folds that occur naturally in the tonsils. The average adult tonsil has anywhere from 10 to 20 crypts. Crypts in the tonsils are usually small and debris free. The tonsil crypts would appear as lines in the tonsils where two edges of the folds meet.

Tonsil stone symptoms
Verywell / Cindy Chung


Crypts in the tonsils are normal, however, they can accumulate food, mucus, and other debris which can lead to the formation of tonsil stones (tonsilloliths) and the following four symptoms:

  • Bad breath (halitosis)
  • A feeling of having something stuck in your throat
  • A chronic sore throat
  • Finding foul-smelling cheese-like clumps in your mouth

The crypts have low levels of oxygen making the environment susceptible to bacteria that do not need oxygen (anaerobes). When a mixture of bacteria starts to accumulate in the crypt, it is possible for an infection to occur.

The infection can cause inflammation which is sometimes referred to as chronic caseous tonsillitis or fetid tonsils. The "caseous" refers to a cheese-like formation in the tonsillar crypts. When the accumulated bacteria, mucus, or other debris does not dissipate, it can calcify and form stones.

Tonsil stones can look like yellowish flecks at the back of the throat. Some are large enough to protrude from the tonsils, resembling tiny rocks of up to a half centimeter (0.2 inches).


You can get cryptic tonsils because you have naturally wrinkly tonsils, which are more prone to trap food. Other debris can accumulate in these holes in your tonsils as well, including pus and bacteria that produce volatile sulfur compounds and creates bad breath.

Of all the causes of bad breath, cryptic tonsils only account for about 3% of cases. Cryptic tonsils often look similar to strep throat or other throat infections. Fortunately, cryptic tonsils alone are not generally harmful to your health.


There are a couple of options for treating cryptic tonsils, depending on the severity of the condition. The standard of care for bothersome tonsil stones is to have them removed by a professional otolaryngologist (ear, nose, throat doctor) or a dentist. Occasionally a general practitioner might be able to remove your tonsil stones.

You should never try to remove a tonsil stone on your own. Using a Waterpik may only force a stone deeper into the tissues. Tongue depressors, tweezers, dental picks, and even cotton swabs are more likely to cause harm than not.

Tonsil Stone Removal

Common methods a healthcare provider may use to remove tonsil stones include irrigation with saline, curettage (using a curette to scoop the stone out), or expressing the stone out manually with a sterile swab.

Another treatment for cryptic tonsils is carbon dioxide laser cryptolysis. This is an in-office procedure which uses a laser beam to ablate (remove) the pockets in the tonsils.

You will be given a local anesthetic to prevent pain during the procedure, which will generally take about 20 minutes. The laser works like peeling an onion. By doing so, it exposes the crypt and allows for the removal of the tonsil stone.

Following the procedure, you will be asked to use over-the-counter analgesics and gargle topical anesthetics for pain control, as well as gargle an antibiotic to prevent infection.

Tonsillectomy Surgery

The last option to treat cryptic tonsils is a tonsillectomy. Removing the tonsils is effective virtually 100% of the time, but the surgery has risks that must be considered.

Tonsillectomy is usually only recommended if your symptoms are unresponsive to more conservative treatments or are exacerbated by sleep apnea, chronic strep throat, or other chronic conditions affecting the throat.

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5 Sources
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  3. Bollen CM, Beikler T. Halitosis: the multidisciplinary approach. Int J Oral Sci. 2012;4(2):55-63. doi:10.1038/ijos.2012.39

  4. Krespi, Y.P. & Kizhner, V. Laser tonsil cryptolysis: In-office 500 cases review. American Journal of Otolaryngology. 2013; 34(5), 420–424. doi:10.1016/j.amjoto.2013.03.006

  5. Siber S, Hat J, Brakus I, et al. Tonsillolithiasis and orofacial pain. Gerodontology. 2012;29(2):e1157-60. doi:10.1111/j.1741-2358.2011.00456.x

Additional Reading
  • Wetmore, RF. Tonsils and Adenoids. In: Kliegman RM, Stanton BF, St Geme JW, Schor NF, Behrman RE, editors. Nelson Textbook of Pediatrics. 20. New York: Elsevier; 2015. pp. 2023-2026.