We demonstrate a selective atomic layer deposition of TiO2, ZrO2, and ZnO thin films on patterned alkylsiloxane self-assembled monolayers. Microcontact printing was done to prepare patterned monolayers of the alkylsiloxane on Si substrates. The patterned monolayers define and direct the selective deposition of the metal oxide thin films using atomic layer deposition. The selective atomic layer deposition is based on the fact that the metal oxide thin films are selectively deposited only on the regions exposing the silanol groups of the Si substrates because the regions covered with the alkylsiloxane monolayers do not have any functional group to react with precursors.