Conditional gene targeting in mice by means of Cre-loxP strategy represents a powerful approach to study mammalian gene function. This approach is however dependent on the availability of suitable strains of mice with a tissue or time restricted activity of the Cre recombinase. Here we describe Aldh3-Cre transgenic mice as a useful tool to conditionally delete genes in cornea, a specialized transparent tissue found on the anterior-most part of the eye, which acts as a protective barrier and contributes to the refractive power. Using a set of floxed alleles we demonstrate high Aldh3-Cre activity in corneal epithelial cells, corneal stroma and conjunctival epithelial cells at postnatal stages. Aldh3-Cre will thus be particularly beneficial for functional analysis of genes which are vital for postnatal development of cornea and conjunctiva.