Examples of congenital disorders which affect the tongue include:

- Aglossia - complete absence of the tongue at birth

- Ankyloglossia (tongue tie) - where the lingual frenum tethers the tongue to the floor of the mouth. If it interferes with oral hygiene and feeding, frenectomy may be indicated.

- Hypoglossia - congenitally short tongue

- Microglossia

- Macroglossia - an abnormally large tongue, seen in some disorders such as Down syndrome (although macroglossia can be an acquired condition as well).

- Hamartomata - for example Leiomyomatous hamartoma

- Glossoptosis

- Choristomata - For example, osseous choristoma of the tongue, a very rare condition characterized by a nodule on the dorsum of the tongue containing mature lamellar bone without osteoblastic or osteoclastic activity. Cartilagenous (chondroid), and glial choristomas may also very rarely occur on the tongue.

- Lingual thyroid

- Cleft tongue (bifid tongue) - completely cleft tongue is a rare condition caused by a failure of the lateral lingual swellings to merge. More common is an incompletely cleft tongue, appearing as midline fissure. This is normally classed as fissured tongue.

Although it may be asymptomatic, symptoms usually are more likely to be present and more severe with larger tongue enlargements. Signs and symptoms include:

- Dyspnea - difficult, noisy breathing, obstructive sleep apnea or airway obstruction

- Dysphagia - difficulty swallowing and eating

- Dysphonia - disrupted speech, possibly manifest as lisping

- Sialorrhea - drooling

- Angular cheilitis - sores at the corners of the mouth

- Crenated tongue - indentations on the lateral borders of the tongue caused by pressure from teeth ("pie crust tongue")

- Open bite malocclusion - a type of malocclusion of the teeth

- Mandibular prognathism - enlarged mandible

- Mouth breathing

- Orthodontic abnormalities - including diastema and tooth spacing

A tongue that constantly protrudes from the mouth is vulnerable to drying out, ulceration, infection or even necrosis.

The ICD-10 lists macroglossia under "other congenital malformations of the digestive system". Definitions of macroglossia have been proposed, including "a tongue that protrudes beyond the teeth during [the] resting posture" and "if there is an impression of a tooth on the lingual border when the patients slightly open their mouths". Others have suggested there is no objective definition of what constitutes macroglossia. Some propose a distinction between "true macroglossia", when histologic abnormalities correlate with the clinical findings of tongue enlargement, and "relative macroglossia", where histology does not provide a pathologic explanation for the enlargement. Common examples of true macroglossia are vascular malformations, muscular enlargement and tumors; whilst Down syndrome is an example of relative macroglossia. "Pseudomacryglossia" refers to a tongue that is of normal size but gives a false impression of being too large in relation to adjacent anatomical structures. The Myer classification subdivides macroglossia into generalized or localized.

The clinical appearance is considerably varied in both the orientation, number, depth and length of the fissure pattern. There are usually multiple grooves/furrows 2–6 mm in depth present. Sometimes there is a large central furrow, with smaller fissures branching perpendicularly. Other patterns may show a mostly dorsolateral position of the fissures (i.e. sideways running grooves on the tongue's upper surface). Some patients may experience burning or soreness.

It presents itself in the mouth, most frequently as a thick, bilateral, symmetrical white plaques with a spongy, corrugated or velvety texture. Most usually, the lesions are on the buccal mucosa, but sometimes on the labial mucosa, alveolar ridge, floor of the mouth, ventral surface of the tongue or soft palate. The gingival margin and dorsum of the tongue are almost never affected. Less commonly, sites outside the mouth are affected, including the nasal, esophageal, laryngeal, anal and genital mucosae. It usually is present from birth, or develops during childhood. Rarely, the lesions may develop during adolescence. Apart from the appearance of the affected areas, there are usually no other signs or symptoms.

Crenated tongue (also called scalloped tongue, pie crust tongue, lingua indentata, or crenulated tongue) is a descriptive term for the appearance of the tongue when there are indentations along the lateral borders (the sides), as the result of compression of the tongue against the adjacent teeth.

The oral mucosa in the area of crenation is usually of normal color, but there may be erythema (redness) if exposed to a high degree of friction or pressure. Crenated tongue is usually asymptomatic and harmless.

It is not a disease as such, but usually results from habits where the tongue is pressed against the lingual surfaces (the side facing the tongue) of the dental arches, or from any cause of macroglossia (enlarged tongue), which in itself has many causes such as Down syndrome.

Where crenation is caused by parafunctional habits, there may also be associated bruxism, linea alba, or morsicatio buccarum.

Tongue diseases can be congenital or acquired, and are multiple in number. Considered according to a surgical sieve, some example conditions which can involve the tongue are discussed below. Glossitis is a general term for tongue inflammation, which can have various etiologies, e.g. infection.

Fissured tongue (also known as "scrotal tongue," "lingua plicata," "Plicated tongue," and "furrowed tongue") is a benign condition characterized by deep grooves (fissures) in the dorsum of the tongue. Although these grooves may look unsettling, the condition is usually painless. Some individuals may complain of an associated burning sensation.

It is a relatively common condition, with a prevalence of between 6.8% and 11% found amongst children. Often hereditary, may also be part of degenerative process. The prevalence of the condition increases significantly with age, occurring in 40% of the population after the age of 40.

There are three grades of inverted nipples, defined on how easily the nipple may be protracted and the degree of fibrosis existent in the breast as well as the damage it has caused on the milk ducts.

Inverted nipple Grade 1 refers to nipples that can easily be pulled out, by using finger pressure around the areola. The Grade 1 inverted nipple maintains its projections and rarely retracts. Also, Grade 1 inverted nipples may occasionally pop up without manipulation or pressure. Milk ducts are usually not compromised and breast feeding is possible. These are "shy nipples". It is believed to have minimal or no fibrosis. There is no soft-tissue deficiency of the nipple. The lactiferous duct should be normal without any retraction.

Inverted nipple Grade 2 is the nipple which can be pulled out, though not as easily as the Grade 1 inverted nipple but which retracts after pressure is released. Breast feeding is usually possible even though it is more likely to be either hard to get the baby to latch comfortably in the first weeks after birth; extra help may be needed. Grade 2 nipples have a moderate degree of fibrosis. The lactiferous ducts are mildly retracted but do not need to be cut for the release of fibrosis. On histological examination, these nipples have rich collagenous stromata with numerous bundles of smooth muscle. Most people with this problem suffer from inverted nipples Grade 2.

Inverted nipple Grade 3 describes a severely inverted and retracted nipple which can rarely be pulled out physically and which requires surgery in order to be protracted. Milk ducts are often constricted and breast feeding is difficult but not necessarily impossible. With good preparation and help often babies can drink at the breast and milk production is not affected; after breastfeeding often nipples are less or no longer inverted. People with Grade 3 inverted nipples may also struggle with infections, rashes, or problems with nipple hygiene. The fibrosis is remarkable and lactiferous ducts are short and severely retracted. The bulk of soft tissue is markedly insufficient in the nipple. Histologically, there are atrophic terminal duct lobular units and severe fibrosis.

An inverted nipple (occasionally invaginated nipple) is a condition where the nipple, instead of pointing outward, is retracted into the breast. In some cases, the nipple will be temporarily protruded if stimulated. Women and men can have inverted nipples.

White sponge nevus (WSN, or white sponge naevus, Cannon's disease, hereditary leukokeratosis of mucosa, white sponge nevus of Cannon, familial white folded dysplasia, or oral epithelial nevus), is an autosomal dominant condition of the oral mucosa (the mucous membrane lining of the mouth). It is caused by a mutations in certain genes coding for keratin, which causes a defect in the normal process of keratinization of the mucosa. This results in lesions which are thick, white and velvety on the inside of the cheeks within the mouth. Usually, these lesions are present from birth or develop during childhood. The condition is entirely harmless, and no treatment is required.

Dental open bite occurs in patients where the anterior teeth fail to touch. However, this is not accompanied by the skeletal tendency of having an open bite. Thus this type of open bite may happen in patients who have horizontal or hypodivergent growth pattern. These patients have normal jaw growth and do not have the long face syndrome. The anterior open bite in these patients may be caused by Macroglossia, Tongue thrusting habit or digit sucking habits. Some of the characteristics of a dental open bite include:

- Normal lower anterior facial height

- Horizontal/Hypodivergent growth pattern

- Occlusal plane diverges after the premolar contact

- Under-eruption of the anterior incisors

- Over-eruption of the posterior incisors

- Proclined upper and lower incisors

- No vertical maxillary excess or gummy smile

- Presence of habits such as thumb sucking, tongue thrusting

- Spacing between anterior incisors due to their proclination

A persistent thyroglossal duct is a usually benign medical condition in which the thyroglossal duct, a structure usually only found during embryonic development, fails to atrophy. The duct persists as a midline structure forming an open connection between the back of the tongue and the thyroid gland.This opening can lead to fluid accumulation and infection, which necessitate the removal of the duct.

In traditional Chinese medicine, scalloping of the tongue is said to indicate qi vacuity. In some homeopathic sources, scalloping of the tongue is said to be indicative of high blood pressure.

Patient with skeletal open bites that accompany dental open bites may have Adenoid faces or Long face syndrome. They are said to have what is known as "Hyperdivergent Growth Pattern" which includes characteristics such as:

- Increased Lower Anterior Facial Height

- Occlusal plane diverges after the 1st molar contact

- May accompany dental open bite

- Narrow nostrils with upturned nose

- Dolicofacial or Leptoprosopic face pattern

- Constricted maxillary arch

- Bilateral Posterior Crossbite

- High and narrow palatal vault

- Presence of crowding in teeth

- Mentalis muscle strain upon forcibly closing of lips

- Possible gummy smile with increased interlabial gap

Cephalometric analysis features of skeletal open bite may include:

- Increased Frankfurt-Mandibular Plane angle

- Steep Occlusal Plane Angle

- Increased SN-MP Angle

- Short Mandibular ramus

- Increased mandibular body length

- Downward and backward position of mandible

- Increased gonial angle

- Proclined upper incisors, retroclined or upright lower incisors

- Posterior part of maxilla is tipped downwards

- Posterior facial height equals 1/2 of anterior facial height

- Increased hard tissue Lower Anterior Facial Height

- Increased total anterior facial height

- Short mandibular ramus

Viken Sassouni developed Sassouni analysis which indicates that patient's with long face syndrome have 4 of their bony planes (mandibular plane, occlusal plane, palatal plane, SN plane) steep to each other.

Congenital epulis is a proliferation of cells most frequently occurring on the alveolar ridge of the upper jaw at birth. Less frequently the mass may arise from the mandibular alveolus. Rare cases can arise from the tongue. This lesion is more commonly found in female babies, suggesting hormonal involvement during embryonic development. The cause of this type of epulis is unknown. Also known as congenital granular cell tumor or Neumann's tumor; historically referred to as granular cell myoblastoma.

Multiple lesions occur in 10% of affected neonates. The tumor is typically pedunculated and varies in maximum size from 0.5 cm to 9 cm. The lesion is typically painless and does not increase in size after discovery. Some small lesions may regress over time. Treatment is surgical excision. Recurrence is extremely rare even after incomplete excision.

Labial fusion is never present at birth, but rather acquired later in infancy, since it is caused by insufficient estrogen exposure and newborns have been exposed to maternal estrogen "in utero". It typically presents in infants at least 3 months old. Most presentations are asymptomatic and are discovered by a parent or during routine medical examination. In other cases, patients may present with associated symptoms of dysuria, urinary frequency, refusal to urinate, or post-void dribbling. Some patients present with vaginal discharge due to pooling of urine in the vulval vestibule or vagina.

The primary (baby) teeth generally start coming in by 6 months of age, and all 20 teeth may be in by two and a half years of age. The eruption timing varies greatly. There may be an incomplete formation of the enamel on the teeth (enamel hypoplasia) that makes the teeth more vulnerable to caries (cavities). There may be missing teeth eruptions. If the infant is not closing down properly, the lower jaws become more noticeably deficient (micrognathia or retrognathia). The front teeth may not touch when the child closes down because the back teeth have overerrupted or because of incomplete formation of the maxilla. This condition is called an anterior open bite and has facial/skeletal implications. The saliva may be thick, or the infant may have a dry mouth.

Studies done on cadavers claim persistent thyroglossal ducts can be completely asymptomatic and found in 7% of the human adult population. However, the continued presence of the duct can often lead to complications due to infections and fluid buildup. The glands in the mucosa of the duct will continue their secretions until the fluid forms a cyst or exit the duct via the opening in the foramen cecum. Local infections, such as colds, tonsillitis, or inflammation of the lymph nodes in the area can also lead to the accumulation of fluid within the duct. Even if the cyst forms as secondary to another infection and improved after antibiotics, it will often reoccur and require treatment.

Three-fourths of abnormalities within a persistent thyroglossal duct involve the formation of a cyst. If a persistent thyroglossal duct becomes fluid filled it will form a thyroglossal duct cyst, which accounts for 70% of congenital neck masses and is the most likely diagnosis if the mass is along the midline of the neck. These cysts are often diagnosed in children under the age of ten and have no particular gender prevalence. The cysts are normally asymptomatic at this age and are noticed because of the swelling that will move if the patient swallows. Over 80% of these cysts are located at or below the hyoid bone.

Very rarely, the persistent duct can become cancerous, called thyroglossal duct carcinoma. In the case of thyroglossal duct carcinoma, the cancerous cells are ectopic thyroid tissue that has been deposited along the thyroglossal duct and will present as a papillary carcinoma. However, the cells are less likely to metastasize in the cyst, than if they were present in the actual thyroid gland.

The other fourth of abnormalities presents as draining abscess. This is from an infection that will rupture through the skin to allow for adequate drainage of the infected area.

When a child is born with Möbius syndrome, there may be difficulty in closing the mouth or swallowing. The tongue may fasciculate (quiver) or be hypotonic (low muscle tone). The tongue may be larger or smaller than average. There may be low tone of the muscles of the soft palate, pharynges, and the masticatory system. The palate may be arched excessively (a high palate), because the tongue does not form a suction that would normally shape the palate down further. The palate may have a groove (this may be partially due to intubation early on if it is for an extended period of time) or may be cleft (incompletely formed). The opening to the mouth may be small. Feeding problems may become a critical issue early on if adequate nutrition is difficult.

Aglossia (aglossia congenita) is a congenital defect resulting in a partial development or complete absence of a tongue.

Aglossiais commonly associated with craniofacial and limb defects (Adactylia syndrome) and is thought to belong to a family of oromandibular limb hypogenesis syndrome or OLHS. It is believed to be caused by heat-induced vascular disruption near the fourth week of embryonic development.

The first known case was reported in the early 18th century by a member of the prominent De Jussieu family in France and cases to this day remain rare.

The condition can be diagnosed based on inspection of the vulva. In patients with labial fusion, a flat plane of tissue with a dense central line of tissue is usually seen when the labia majora are retracted, while an anterior opening is usually present below the clitoris.

Ankyloglossia, also known as tongue-tie, is a congenital oral anomaly that may decrease mobility of the tongue tip and is caused by an unusually short, thick lingual frenulum, a membrane connecting the underside of the tongue to the floor of the mouth. Ankyloglossia varies in degree of severity from mild cases characterized by mucous membrane bands to complete ankyloglossia whereby the tongue is tethered to the floor of the mouth.

Ankyloglossia can affect eating, speech, and oral hygiene as well as have mechanical/social effects. Ankyloglossia can also prevent the tongue from contacting the anterior palate. This can then promote an infantile swallow and hamper the progression to an adult-like swallow which can result in an open bite deformity. It can also result in mandibular prognathism; this happens when the tongue contacts the anterior portion of the mandible with exaggerated anterior thrusts.

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, and bordered by a slightly raised, white, yellow or grey, serpiginous (snaking) peripheral zone. A lesion of geographic tongue may start as a white patch before the depapillation occurs. In certain cases there may be only one lesion, but this is uncommon; the lesions will typically occur in multiple locations on the tongue and coalesce over time to form the typical map-like appearance. The lesions usually change in shape, size and migrate to other areas, sometimes within hours. The condition may affect only part of the tongue, with a predilection for the tip and the sides of the tongue, 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.

There are usually no symptoms other than the unusual appearance of the tongue, 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). Where there is a burning symptom, other causes of a burning sensation on the tongue are considered, such as oral candidiasis.