The fetal alcohol syndrome involves various neural crest-derived structures thus causing systemic and ocular malformations. This study investigated anomalies of the corneal endothelium, a neural crest-derived tissue, in eight children affected by fetal alcohol syndrome without known anterior segment anomalies. We performed specular biomicroscopy on the central corneal endothelium. The data were then compared with those from 80 age-matched healthy children, applying the same methods. Significant differences were found between patients with fetal alcohol syndrome and healthy subjects for mean cell density (P = .032), polymegethism (P = .000), and percentage of hexagonal cells (P = .000). We also found a close correlation between endothelial anomalies and auditory dysfunction in the patients with fetal alcohol syndrome. These alterations may be a consequence of alcohol-induced toxic effects on neural crest cells destined to form both the corneal endothelium and the organ of Corti in the same embryogenic period.