Epithelial basement membrane corneal dystrophy (EBMD), also known as Cogan microcystic epithelial dystrophy or map-dot-fingerprint dystrophy, is a common bilateral epithelial dystrophy. Usually, this disease is not considered to be inherited although several families with autosomal dominant inheritance have been described. We report the analysis of two families with an autosomal dominant pattern of inheritance as well as the analysis of single affected individuals; we identified two different point mutations in the TGFBI/BIGH3 genes, genes known to be associated with other corneal dystrophies. This is the first report of a molecular mutation in individuals with EBMD and it increases the spectrum of mutations in the TGFBI/BIGH3 gene. Based on our screening, up to 10% of EBMD patients could have a mutation in this gene.