In this study, we showed compound heterozygous mutations of c.287G > A and c.709G> A in the ALDH1A3 gene in a newborn boy with anophthalmia, and theexpression of two mutant proteins was significantly decreased in vitro.ALDH1A3 is a critical dehydrogenase that contributes to the conversion of retinaldehydeto retinoic acid, which is vital in the normal morphogenesis of eye development. Here, ALDH1A3 is linked to Anophthalmia.