We review the central nervous system anatomy in nine cases of amniotic rupture sequence, all of which had neuropathological examinations. Of these, four had normal brains, and in none of these was the cranial vault involved, and one had cleft lip and palate. Of the remaining five, all had portions of the scalp, calvarium and dura replaced by amnionic membrane directly overlying arachnoid. In one, the membrane covered a narrow necked large encephalocele, and the contained brain demonstrated extensive disruption and degeneration. In the remaining four, one demonstrated cranioplacental adhesion, and in three there was a broad based encephalocele covered in large part by amnion. Two of these four cases demonstrated holoprosencephaly. One case with holoprosencephaly and one without demonstrated marked aqueductal stenosis, and two of the four demonstrated aqueductal occlusion or near occlusion by neuroglial excrescences. None demonstrated ventriculomegaly. Three of these four cases demonstrate varying degrees of mechanical distortion and secondary pathology. We conclude that brains with amnionic rupture sequence demonstrate both malformation and deformation, which likely points to the embryonic stage origin of the lesion.