AbstractThe msh‐related homeobox genes, Msx1 and Msx2, have a variety functions during murine organogenesis, Msx1 in the development of the palate and teeth, Msx2 in the skull, teeth, and skin. Msx1 mutants die perinatally. Compound Msx1‐2 mutants do not survive past late gestation. The multiplicity of functions of Msx1 and 2, as well as the lethality of Msx1 and Msx1‐2 mutants limits the utility of the conventional knockouts. We therefore produced conditional alleles of Msx1 and Msx2. We constructed targeting vectors with LoxP sites flanking the homeodomain‐encoding second exons and Frt sites flanking a neo gene. These vectors were used to produce targeted ES cells and mice with floxed alleles. The functionality of the LoxP sites in the floxed alleles was established by crosses with K14‐Cre mice (epidermis‐specific), and with an Msx2‐Cre line that produces a germline deletion. Analysis of progeny by PCR revealed correct Cre‐mediated recombination, as well as expected phenotypes. genesis 45:477–481, 2007. Published 2007 Wiley‐Liss, Inc.