Background: Astacin-like metallo-proteases are zinc endopeptidases conserved among vertebrates and invertebrates. First described as hatching gland enzymes, many members of the family possess other functions during embryonic development. In the chick, however, functions of Astacin-like proteins remain elusive. Results: We report here that Astacin-like (ASTL) is strongly expressed in mouse and chicken embryonic stem (ES) cells and exhibits a very dynamic expression pattern during embryogenesis and organogenesis, mostly in remodeled epithelia. Consistent with its expression in ES cells, chick ASTL is detected in vivo in the pluripotent cells of the epiblast and then disappears from the newly induced neural plate. ASTL expression remains at the junction of non-neural and neural ectoderm, just before neural tube closure. At later stages, chick ASTL is detected in the ventral epidermis before ventral closure, in the intermediate mesoderm, in the gonads and in the forming nephric duct and tubules of the mesonephros and metanephros. Conclusions: ASTL is dynamically expressed in the embryonic epithelium and in embryonic stem cells, suggesting an important function for the control of epithelial cell behavior during early development.