The structure of seed layers has been considered as a significant factor to dictate the subsequent growth of ZnO nanorods. We carefully studied seed layer structures such as crystallinity, surface crystal orientations, and grain sizes to investigate their effect on ZnO nanorod growth during hydrothermal synthesis. The structure of seed layers was changed by controlling their thickness and further annealing treatments at 200-1000 °C. Among several parameters of seed layer structure, the grain size and the surface crystal orientation were found to make a noticeable change in the morphology of ZnO nanorods. Thick ZnO nanorods were produced on large grains while densely aligned products were observed on the seed layer surface with c-axis orientation. In addition, at the early stage of synthesis, we observed ZnO nanorods with a diameter much smaller comparing to the size of grains consisting of poly-and single crystal. This explains that the nucleation of ZnO crystals start on c-axis oriented domains, and they grow in a length favorably and in diameter gradually, resulting in the formation of ZnO nanorods with the integration of tightly aligned products.