We have developed a novel method for site-selective deposition (SSD) of thin films using a seed layer. The deposition process of anatase TiO2 from an aqueous solution was evaluated in detail using a quartz crystal microbalance, and it was found that the nucleation and initial growth of anatase TiO2 were accelerated on amorphous TiO2 thin films compared with silanol, amino, phenyl, or octadecyl groups. Amorphous TiO2 thin films were deposited on silanol regions of a patterned octadecyltrichlorosilane self-assembled monolayer from a titanium dichloride diethoxide solution. This substrate was immersed in an aqueous solution containing Ti precursor to be used as a template for SSD. Anatase TiO2 was selectively deposited on amorphous TiO2 regions to form thin films. Consequently, a micropattern of anatase TiO2 thin film which had high feature edge acuity was successfully fabricated in an aqueous solution.