Rathke's cleft is a remnant of Rathke's pouch, which is an embryological structure that forms during the development of the pituitary gland. During fetal development, Rathke's pouch is a small invagination in the roof of the mouth that grows upward toward the brain and eventually forms the anterior lobe of the pituitary gland (adenohypophysis). The posterior part of Rathke's pouch becomes the intermediate lobe of the pituitary.

In most cases, Rathke's pouch closes off completely, leaving only a small cleft or cavity called Rathke's cleft. In some individuals, however, Rathke's cleft may persist as a larger cystic structure, known as a Rathke's cleft cyst. These cysts are generally benign (non-cancerous) and may not cause any symptoms. However, if they grow large enough, they can compress surrounding structures, leading to symptoms such as headaches, vision problems, or hormonal imbalances.

Rathke's cleft cysts are often discovered incidentally on imaging studies or may be found during surgery for other pituitary-related conditions. Treatment may not be necessary for asymptomatic cysts, but symptomatic cysts may require surgical drainage or removal.