We describe two unrelated patients with severe microcephaly, ACC, and FBD-like cortical malformation, who have inherited deletions of 16p13.11 combined with truncating mutations in NDE1. In all patients reported to date with the homozygous NDE1 phenotype, severe congenital microcephaly was present with profound intellectual disability and early onset seizures. This evidence concerns the gene NDE1 and microcephaly.