Cerebellar vermis hypoplasia (CVH) is part of many different malformation syndromes, especially Joubert syndrome. However, the nosology of these disorders remains uncertain. We reviewed reports of 100 children with cerebellar vermis hypoplasia, and ocular or renal involvement. Although the status of the upper brainstem was not adequately documented in most of these patients, some had hypoplasia and dysplasia of the ponto-mesencephalic isthmus and the superior portion of the cerebellar vermis, which results in a "molar tooth" sign on MRI scan. Several distinct syndromes were apparent among this group. We conclude that (a) hypoplasia of the cerebellar vermis, especially the anterior vermis, is often associated with a complex brainstem malformation; (b) the latter comprises a "molar tooth" brainstem and vermis hypoplasia-dysplasia malformation complex; (c) this complex may include the Dandy-Walker malformation, occipital cephalocele, and some abnormalities of the cerebrum as evidenced by frequent mental retardation; and (d) the "molar tooth" sign or malformation is causally heterogeneous as it occurs in several distinct malformation syndromes including