TiO2 has unique characteristics of high chemical stability, photocatalyst etc. Crystallographically oriented or aligned nano-rod structure is preferable considering the uniformity of function or aiming at the higher performance in the application such as piezoelectric devices though it is difficult to produce. This study demonstrates a simple fabrication process for vertically aligned TiO2 structure using hydrothermal synthesis. A fluorine-doped tin oxide (FTO) substrate was used as a substrate because its lattice constant is close to that of rutile-TiO2. The morphology or thickness of the structure was controlled by changing synthesis conditions such as source material concentration. Vertically aligned TiO2 nano-rods were successfully fabricated of which diameter and height was about 300 nm and 5 μm respectively after four hours synthesis. The variation of the height was examined because the smoothness is sometimes important in the application. Water contact angle on the structure was measured as about 10° and the hydrophilicity persisted for long time comparing with a glass substrate.