<p>Emerging evidence indicates that ion channels and transporters are critical for normal embryonic development. They are essential for establishing membrane potential (V_m), a property of all cells. However, it is uncertain if embryos have germ-layer specific regional differences in electrical behavior that play a role in defining local cell fates. In our study, by manipulating ion concentrations and applying a wide spectrum of inhibitors, we demonstrate that various ion channels and transporters differentially determine V_m in specific germ layers of the <i>Xenopus tropicalis</i> embryo. Altering the electrical properties of the embryo leads to localized changes in cell fate and alterations in left-right patterning, which can lead to severe diseases, including heterotaxy and congenital heart disease. Our results indicate that the electrical properties of early embryonic cells are regionally specified and affect local cell fates.</p>