Diagnosis is usually made upon inspection. Differential diagnosis of tonsilloliths includes foreign body, calcified granuloma, malignancy, an enlarged temporal styloid process or rarely, isolated bone which is usually derived from embryonic rests originating from the branchial arches.

Tonsilloliths are difficult to diagnose in the absence of clear manifestations, and often constitute casual findings of routine radiological studies.

Imaging diagnostic techniques can identify a radiopaque mass that may be mistaken for foreign bodies, displaced teeth or calcified blood vessels. Computed tomography (CT) may reveal nonspecific calcified images in the tonsillar zone. The differential diagnosis must be established with acute and chronic tonsillitis, tonsillar hypertrophy, peritonsillar abscesses, foreign bodies, phlebolites, ectopic bone or cartilage, lymph nodes, granulomatous lesions or calcification of the stylohyoid ligament in the context of Eagle syndrome (elongated styloid process).

Often, no treatment is needed, as few stones produce symptoms.

Some people are able to remove tonsil stones using the tip of the tongue. Oral irrigators are also simple yet effective and will thoroughly clean the tonsil crypts. Most electric oral irrigators are unsuitable for tonsil stone removal because they are too powerful and are likely to cause discomfort and rupture the tonsils, which could result in further complications such as infection. Irrigators that connect directly to the sink tap via a threaded attachment or otherwise are suitable for tonsil stone removal and everyday washing of the tonsils because they can jet water at low pressure levels that the user can adjust by simply turning the sink tap, allowing for a continuous range of pressures to suit each user's specific requirements.

More simply still, gargling with warm, salty water may help alleviate the discomfort of tonsillitis, which often accompanies tonsil stones. Vigorous gargling each morning can also keep the tonsil crypts clear of all but the most persistent tonsilloliths.