This paper presents a novel process for the fabrication of site-selectively deposited tin oxide ultrathin films (<10 nm) by using molecular recognition between the precursors and the surface of the Si substrate. Using this simple technique, the film thickness of micropatterned tin oxide films was easily controlled. Patterned self-assembled monolayers, in which both hydrophilic and hydrophobic areas formed, were used as templates for the site-selective deposition of the films. Two precursors of SnCl4 and C4H9SnCl3 were selected. The films were selectively deposited on the hydrophilic regions through the liquid phase. The growth rate of the film deposited in SnCl4 solution was approximately 6 times faster than that in C4H9SnCl3 solution. A quartz crystal microbalance measurement implied that film growth could be suppressed by the formation of hydrophobic surfaces on the growing films with increasing immersion time in C4H9SnCl3 solution.