Tonsils are the oval-shaped organs found at the back of your throat. They help protect your body from microbial infections. Holes in the tonsils, or tonsillar crypts, have an increased risk of developing infection or tonsil stones.

Holes in the tonsils are a normal part of your anatomy. They give your immune system an early idea of what your body is ingesting by mouth. Sometimes, the tonsils may swell and the crypts can become blocked due to inflammation or scar formation from another condition.

Conditions that can cause the tonsils to become inflamed include:


Tonsillitis is an inflammation of the tonsils. It’s most often caused by viral infections. Bacterial infections may also be the culprit. This condition is particularly common in school-age children and people who work with them.

Additional symptoms of tonsillitis may include:

  • red swollen tonsils
  • white or yellow patches on the tonsils
  • sore throat
  • painful swallowing
  • enlarged lymph nodes
  • bad breath
  • headache
  • stomachache
  • fever


Often called “mono” or “the kissing disease,” mononucleosis is a virus transmitted through saliva. This condition can cause your tonsils to become swollen, and can lead to obstruction of the tonsillar crypts.

Symptoms of mononucleosis include:

  • fatigue
  • sore throat
  • fever
  • headache
  • skin rash
  • tender, swollen spleen

It may take several weeks to recover from mononucleosis.

Strep throat

Strep throat is a highly contagious infection caused by a streptococcus bacterium. It’s very common among school-age children. Strep throat should be treated as soon as possible to avoid complications like kidney inflammation or rheumatic fever.

The telltale symptom that sends most people to the doctor is the unrelenting scratchy sore throat, which often comes on quickly. Some people will have swollen tonsils that are red, with white patches or streaks of pus on them.

Other symptoms include:

  • fever
  • headache
  • rash
  • tiny red spots at the back of the roof of the mouth
  • swollen lymph nodes

Poor oral hygiene

Poor oral hygiene can provide a breeding ground of bacteria that can cause infection and tonsillitis. If you aren’t doing a good enough job of keeping your mouth clean and free of harmful bacteria, your tonsillar crypts may become more frequently filled with bacteria. This can cause the tonsils to become swollen, inflamed, and infected.

Other signs of poor oral hygiene often include frequent bad breath, plaque buildup or coating on the tongue or teeth, and recurrent cavities.

Brush and floss your teeth at least twice a day, and use mouthwash to keep your mouth clean.

Tonsil stones

Tonsil stones (or tonsilloliths) occur when debris becomes trapped in the pits of the tonsils and forms into a white “stone.” These stones can grow. They can also cause further infection in the tonsils, making the holes in the tonsils worse.

Other symptoms of tonsil stones may include:

  • bad breath
  • ear pain
  • trouble swallowing
  • persistent cough
  • white or yellow debris on the tonsil


Smoking and vaping wear down your immune system while simultaneously causing inflammation. This leaves you susceptible to bacterial and fungal infection, as well as inflammation in the tonsils.

Smoking is also linked to tonsil stones, which can make the holes in your tonsils larger and more problematic.

Oral and tonsil cancer

Oral cancer that spreads to the tonsils, and tonsil cancer, can both be associated with holes in the tonsils. Sometimes, the cancer is caught because it results in a sore in the back of the mouth that won’t heal.

Other symptoms of oral and tonsil cancers include:

  • one tonsil being larger than the other
  • blood in the saliva
  • persistent sore throat
  • mouth pain
  • severe ear pain
  • lump in the neck
  • pain when swallowing
  • bad breath

To keep holes in the tonsils from becoming infected, here are several things you can do:

  • Gargle with salt water. Gargling can ease inflammation and reduce discomfort.
  • Practice good oral hygiene. Good hygiene will help prevent infection and may prevent additional holes from forming.
  • Stop smoking immediately. If you’re smoking or using any type of tobacco products, stop as soon as possible.
  • Use mouthwash. Mouthwash can help reduce infections.

If your tonsils become infected, treatment will depend on what is causing the infection. Some infections may not require any treatment unless they’re causing further problems. Some conditions do require treatment, including:

  • Strep throat. This condition is treated with antibiotics.
  • Mononucleosis. You will need to rest a great deal and drink plenty of water if you have this condition.
  • Oral cancer. Doctors typically treat this condition with a combination of surgery (to remove the cancer), chemotherapy, and radiotherapy.
  • Tonsil stones. You can dislodge tonsil stones with salt water gargles. If this doesn’t work, your doctor can remove them using lasers or sound waves.

If holes in the tonsils or their side effects — including tonsil stones or infection — become too prevalent, your doctor may recommend surgical removal. This isn’t as common as it used to be, but it still has a short recovery time of about one week.

The most effective way to deal with holes in the tonsils is to avoid risk factors for infection. Practice good oral hygiene, stop smoking, and wash your hands frequently to avoid viruses and infections whenever possible.

If you notice any blisters, pus, or white spots on your tonsils, make an appointment with your doctor. The Healthline FindCare tool can provide options in your area if you don’t already have a doctor. In the meantime, gargling with salt water and keeping your mouth as clean as possible can promote healing and prevent infection.