What to Do About Cryptic Tonsils

Tonsillar crypts are pockets or folds that occur naturally in tonsils, which are lumps of soft tissue on each side of the throat that are part of the immune system.

Crypts in the tonsils are usually small and debris-free. However, if food, mucus, and other debris collects in them and gets stuck, it can harden into tonsil stones, also called tonsilloliths.

This article will explore common symptoms, causes, and treatment for tonsil stones that form in the crypts.

Tonsil stone symptoms
Verywell / Cindy Chung

Symptoms of Tonsil Stones in Cryptic Tonsils

Most tonsil stones are harmless and do not lead to pain. If they are small, they may not cause any symptoms.

If there are symptoms, they can include:

  • Bad breath (halitosis)
  • Cough
  • A feeling of having something stuck in your throat
  • A chronic sore throat
  • Finding foul-smelling cheese-like clumps in your mouth
  • Ear pain
  • Throat infections that are hard to treat with antibiotics

Bad breath is the most common symptom of tonsil stones.

Tonsil stones can look like white or yellowish flecks at the back of the throat. Some are large enough to stick out from the tonsils, resembling tiny rocks.

The crypts have low levels of oxygen, making the environment susceptible to bacteria that do not need oxygen, which are called anaerobes. When a mixture of bacteria starts to build up in the crypt, it can lead to an infection.

The infection can cause inflammation that is sometimes referred to as chronic caseous tonsillitis or fetid tonsils.

The "caseous" refers to a cheese-like formation in the crypts. If this cheese-like mix of bacteria, mucus, or other debris does not go away, it can harden or calcify into stones.


You can get an infection or tonsil stones in the crypts if you have naturally wrinkly tonsils, which are more prone to trapping food.

Other debris can build up in these holes in your tonsils as well, including pus—a thick fluid that is part of the body's inflammatory response to an infection—and bacteria that produce sulfur compounds and create bad breath.

Cryptic tonsils account for only about 3% of cases of bad breath, though.

Inflamed cryptic tonsils often look similar to strep throat or other throat infections. Fortunately, cryptic tonsils alone are not generally harmful to your health.

Folds in tonsils called crypts are normal. If food and other material gets trapped in the crypts, it can lead to infections or harden into tonsil stones, causing bad breath and/or throat irritation.

How to Treat Tonsil Stones in Cryptic Tonsils

There are several options for removing tonsil stones if you have cryptic tonsils, depending on the severity of the condition.

Tonsil stones are typically removed by an otolaryngologist (ear, nose, throat doctor) or a dentist. Occasionally, a general practitioner might be able to remove your tonsil stones.

Do not 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, or rinsing it with a salt water solution
  • Curettage, or using a tool called a curette to scoop the stone out
  • Expressing the stone out manually with a sterile swab
  • Carbon dioxide laser cryptolysis, an in-office procedure that uses a laser beam to remove the pockets in the tonsils

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

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

Tonsillectomy Surgery

The last option to treat cryptic tonsils is surgical removal of the tonsils, which is called a tonsillectomy.

Removing the tonsils is highly effective, but the surgery has risks that must be considered, such as a risk of bleeding after the procedure. It also may include general anesthesia, which puts you into a sleep-like state for the surgery.

Tonsillectomy is usually only recommended if other treatments weren't effective or if you have additional conditions such as sleep apnea (pauses in breathing during sleep), chronic strep throat, or other chronic conditions affecting the throat.


If food and debris gets trapped in the pockets and folds of your tonsils, it can harden into yellow or white deposits called tonsil stones.

Tonsil stones in the crypts are usually harmless but can lead to bad breath and throat irritation.

It's not recommended to try to remove a tonsil stone on your own. An ear, nose, and throat specialist or dentist can use tools to remove them safely and fully.

7 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
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Additional Reading
  • Wetmore, RF. Tonsils and Adenoids. In: Kliegman RM, Stanton BF, St Geme JW, Schor NF, Behrman RE, editors. Nelson Textbook of Pediatrics. New York: Elsevier; 2015: 2023-2026.

By Kristin Hayes, RN
Kristin Hayes, RN, is a registered nurse specializing in ear, nose, and throat disorders for both adults and children.