Iniencephaly is a rare congenital malformation consisting of a complex alteration of the embryonic development occurring around the third post-fertilization week and characterized by a hyper-retroflexion of the cephalic pole. We report a case of iniencephaly associated with acrania-encephalocele, spina bifida and abnormal ductus venosus in a fetus with trisomy 18 diagnosed at 12 week's gestation in a 41-year-old woman. A co-occurrence between aneuploidy and iniencephaly was documented and polymorphisms on folate metabolism-related genes were investigated in the parents to assess possible etiologic factors and recurrence risk for neural tube defects (NTD). An homozygous state for the MTRR polymorphism was diagnosed in the mother, identifying a clinical risk for NTD. Once iniencephaly or any other NTD are suspected, genetic analysis, second level ultrasound and fetal karyotype are recommended. Autopsy should also be performed in all cases of early ultrasound-based diagnosis of fetal malformations.