In health, the dorsal surface of the tongue is covered in tuft like projections called lingual papillae (some of which are associated with taste buds), which give the tongue an irregular surface texture and a white-pink color. Geographic tongue is characterized by areas of atrophy and depapillation (loss of papillae), leaving an erythematous (darker red) and smoother surface than the unaffected areas. The depapillated areas are usually well demarcated,^[4] and bordered by a slightly raised, white, yellow or grey, serpingious (snaking) peripheral zone.^[10] A lesion of geographic tongue may start as a white patch before the depapillation occurs.^[4] Sometimes there may be only one lesion, but this is uncommon,^[4] and more usually the lesions may start at multiple different locations on the tongue, and then over time the areas coalesce to form the typical map-like appearance. The lesions usually change in shape, size and migrate to other areas, sometimes within hours.^[11] The condition may affect only part of the tongue, with a predilection for the tip and the sides of the tongue,^[4] or the entire dorsal surface at any one time. The condition goes through periods of remission and relapse. Loss of the white peripheral zone is thought to signify periods of mucosal healing.^[10]

There are usually no symptoms, but in some cases persons may experience pain or burning e.g. when eating hot, acidic, spicy or other kinds of foods (e.g. cheese, tomatoes, fruit).^[1][11] Where there is a burning symptom, other causes of a burning sensation on the tongue are considered, such as oral candidiasis.^[9]

The cause is unknown.^[12][1][13] Geographic tongue does not usually cause any symptoms, and in those cases where there are symptoms, an oral parafunctional habit may be a contributory factor.^[10] Persons with parafunctional habits related to the tongue may show scalloping on the sides of the tongue. Some suggest that hormonal factors may be involved,^[2] because one reported case in a female appeared to vary in severity in correlation with oral contraceptive use.^[4] People with geographic tongue frequently claim that their condition worsens during periods of psychologic stress.^[10] Geographic tongue is inversely associated with smoking and tobacco use.^[12] Sometimes geographic tongue is said to run in families,^[2] and it is reported to be associated with several different genes, though studies show family association may also be caused by similar diets. Some have reported links with various human leukocyte antigens, such as increased incidence of HLA-DR5, HLA-DRW6 and HLA-Cw6 and decreased incidence in HLA-B51.^[11] Vitamin B2 deficiency (ariboflavinosis) can cause several signs in the mouth, possibly including geographic tongue,^[14] although other sources state that geographic tongue is not related to nutritional deficiency.^[2] Fissured tongue often occurs simultaneously with geographic tongue,^[1] and some consider fissured tongue to be an end stage of geographic tongue.^[10]

In the past, some research suggested that geographic tongue was associated with diabetes, seborrheic dermatitis and atopy, however more modern research does not corroborate these findings.^[12] Some studies have reported a link between geographic tongue and psoriasis,^[15] although 90% of children who are diagnosed with geographic tongue do not contract psoriasis.^[13] Again however, modern research studies do not support any link between psoriasis and geographic tongue.^[12] Lesions that are histologically indistinguishable from geographic tongue may also be diagnosed in Reiter's syndrome (arthritis, uveitis/conjunctivitis and urethritis).^[10]