This article describes a classification and imaging diagnosis of intracranial midline cystic malformations based on neuroembryologic analysis. Midline cystic malformations are classified into two categories from an embryologic point of view. In one category, the cyst represents expansion of the roof plate of the brain vesicle, and in the other the cyst consists of extraaxial structures such as an arachnoid membrane or migrating ependymal cells. Infratentorial cysts, such as the Dandy-Walker cyst or Blake's pouch cyst, and supratentorial cysts, such as a communicating interhemispheric cyst with callosal agenesis or a dorsal cyst with holoprosencephaly, are included in the first category. Infratentorial arachnoid cavities, such as the arachnoid cyst, arachnoid pouch, and mega cisterna magna, are in the second category. Noncommunicating interhemispheric cysts, such as interhemispheric arachnoid cyst or ependymal cyst, with callosal agenesis are also in the second category. A careful review of embryologic development is essential for understanding these midline cysts and for making a more accurate radiologic diagnosis.