Tonsils are gland-like organs at the back of your throat. Holes are actually a natural occurring part of the tonsils as your tonsils are filled with folds, recesses and holes thought to filter bacteria and viruses passing through your throat. However, in people who have chronic tonsillitis or other throat infections, the holes can become too large, leaving room for this debris to become trapped and harden into tonsil stones. While surgically removing tonsils is the only way to cure the holes, less drastic steps can help manage the issues they cause.

Treatment and Prevention

Because they are naturally occurring constructs of the tonsils, the only way to truly eliminate these holes is through a tonsillectomy, the surgical removal of the tonsils. However, a tonsillectomy is a procedure conducted under general anesthesia and has the potential for other complications, excess bleeding and several days of discomfort and recovery. For that reason, most doctors recommend other less invasive measures to manage the results of holes in tonsils. In most cases, people are able to remove larger tonsil stones at home using a cotton swab or dental pick. Other methods include gargling with a non-alcohol-based mouthwash and using a Waterpik as a small power wash to loosen the stone. Gargling with a warm salt-water solution may relieve some of the pain from tonsillitis that often comes with tonsil stones. As tonsil stones become more chronic, painful or difficult to manage, some doctors may recommend an antibiotic to treat them. Finally, in cases where the stones have gotten too large to be removed at home, they can be surgically removed. A doctor can do this simple procedure with a local anesthesia without other complications or the need for long recovery.

Source:

WebMD: Tonsil Stones

New York Times: In Tonsils, a Problem the Size of a Pea