Brain imaging now provides exquisite images of the central nervous system (CNS) enabling identification of CNS malformations early during pregnancy. However, pathogenical evaluation, necessary for genetic counselling, requires a detailed neuropathological analysis. Brain imaging of a female fetus at 27 weeks gestation disclosed a paramedial cystic formation, considered to be a porencephalic lesion. Neuropathological correlation after pregnancy termination disclosed partial atresia of the third ventricle, responsible for lateral ventricle dilatation and corpus callosum lamination. Atresia of the third ventricle, that we suggest could be called "diencephalo-synapsis", is a rare CNS malformation due to an unknown cause. Further neuropathological studies and phenotype-genotype correlations are necessary for the delineation of the entity and the comprehension of its cause and pathogenesis.