Hypoglossia is a short, incompletely developed tongue. It can occur either as an isolated malformation or in association with other deformities, particularly limb defects in a syndrome known as "oromandibular limb hypogenesis syndrome".

Tongue lesions are very common. For example, in the United States one estimated point prevalence was 15.5% in adults. Tongue lesions are more common in persons who wear dentures and tobacco users. The most common tongue conditions are geographic tongue, followed by fissured tongue and hairy tongue.

Hippocrates, Galen and others considered the tongue to be a "barometer" of health, and emphasized the diagnostic and prognostic importance of the tongue. Assessment of the tongue has historically been an important part of a medical examination. The shape and color of the tongue is examined and observed diagnostically in traditional Chinese medicine. For example, scalloping of the tongue is said to indicate qi vacuity. Some modern medical sources still describe the tongue as "the mirror of physical health". This is related to the high rate of turnover of the oral mucosa compared to the skin, which means that systemic conditions may manifest sooner in the mouth than the skin. Physical appearances such as cyanosis are also often more readily apparent in the mouth.

Hanhart syndrome (also known as Aglossia adactylia; Hypoglossia-hypodactylia syndrome; Peromelia with micrognathia) is a congenital disorder that causes an undeveloped tongue and malformed extremities and fingers.