Patterned growth of vertically aligned ZnO nanowire arrays on the micrometer and nanometer scale on sapphire and GaN epilayers is reported. In order to control the position and distribution density of the ZnO nanowires, Au seeding nanodots are defined, as regular arrays, with the assistance of deposition shadow masks. Electron micrographs reveal that the wires are single crystals having wire axes along the hexagonal c -axes. The epitaxial growth of ZnO nanowires on sapphire and GaN films on Si substrates was further verified by cross sectional electron microscopy investigations. Compared to the sapphire case, the perfect epitaxial growth on a GaN film on a Si substrate is believed to be more suitable for potential electronic device applications of ZnO nanowire arrays.