Cleft palate, also known as palatoschisis, is a type of congenital defect that affects between 0.1% to 0.2% of the horse population. It is the malformation of the soft and sometimes hard palate where the left and right side fail to unite, forming a cleft. Although cleft palate is considered to be uncommon in horses, it is one of the most common craniofacial defect in congenitally deformed foals and fetuses. Between 1 to 4% of foals are born with congenital defects.

Cleft palate occurs in a wide range of animal species, including humans. The cause is not well understood, and is thought to be multi-factorial, and is associated with genetics, environmental, metabolic, hormonal, nutritional, and exposure to toxins. In cattle and pigs, the occurrence of cleft palate in offspring has been associated with ingestion of certain toxic plants (such as poison hemlock, wild tobacco tree, lupines, and wild parsnip), an autosomal recessive trait, selenium and manganese deficiencies, bovine viral diarrhea virus, and akabane virus infections. In cattle, cleft palates often occur concurrently with arthrogryposis.

In horses, cleft palate most commonly affects the caudal 1/2 to 2/3rds of the foal's soft palate. The extent of clinical signs varies depending on the severity of the defect. The most common clinical signs in foals are difficulty swallowing with nasal discharge of milk occurring in both nostrils, immediately after nursing.