CDP/Cut homeodomain factors are a divergent group of transcriptional repressors that are conserved during metazoan evolution. The cut locus of Drosophila is required for external sensory organ development and dorso-ventral boundary formation in the wing. In vertebrates, two CDP/Cut genes have been identified, Cux1 and Cux2. While Cux1 is widely expressed in mouse embryos particularly in the nephrogenic and urogenital systems, in contrast the early embryonic expression of Cux2 has not been characterized. Here we describe the dynamic profile of Cux2 during mouse embryogenesis. Cux2 expression becomes elaborated in a number of tissues during organogenesis including the olfactory epithelium, branchial arch and limb bud progress zones, roof plate, motor neurons, dorsal root ganglia and urogenital tissues. The conservation of signaling pathways between the branchial arches and limb buds is well documented and surprisingly this can also be applied to the developing urogenital system. Cux2 expression coincides with many tissue regions undergoing proliferative growth or cell rearrangements, however some later expression domains also include sites of programmed cell death. Cux2 is hypothesized to function as a transcriptional regulator that inhibits terminal differentiation and cell cycle exit.