In this paper, hydrothermal synthesis combined with microfabrication techniques is used for growing vertically-aligned zinc oxide (ZnO) nanowires (NWs) on zinc (Zn) seed layers patterned on silicon (Si) and polyimide (PI). The NWs have shown a hexagonal crystalline structure and vertical orientation. The substrate material together with the hydrothermal precursor concentration has shown to influence the diameter and length of the NWs. Atomic force microscopy and scanning electron microscopy have revealed that the substrate material affects the grain size of the deposited seeds and consequently the morphology of the NWs which show a diameter in the range 100–220 nm and 130–400 nm when grown on Si and PI, respectively. NWs grown with an optimised concentration of 2 mM are densely packed and vertically-aligned with a consistent uniform distribution on both types of substrates.