A method of forming an organic thin film transistor is disclosed. The method includes forming source and drain electrodes on a substrate; forming an insulating layer covering the source and drain electrodes; first surface-treating the insulating layer so that the insulating layer has a hydrophobic surface; forming an opening that exposes facing portions of the source and drain electrodes in the first surface-treated insulating layer; forming an organic semiconductor layer and a gate insulating layer in the opening; second surface-treating the first surface-treated insulating layer so that the insulating layer has a hydrophilic surface; and forming a gate electrode overlapping at least a portion of the source and drain electrodes, an organic thin film transistor, and a flat panel display device including the organic thin film transistor. According to the method of preparing an organic thin film transistor as described above, at least one of an organic semiconductor layer and a gate insulating layer can be easily formed. When the organic thin film transistor is formed in an array form with respect to a capacitor, the organic thin film transistor has a substantially low parasitic capacitance and the capacitor has a high capacitance.