An organic thin film transistor that can reduce contact resistance between source and drain electrodes and an organic semiconductor layer and can be readily manufactured, a flat panel display apparatus utilizing the organic thin film transistor, and a method of manufacturing the organic thin film transistor. The organic thin film transistor includes: a substrate; a source electrode and a drain electrode disposed on the gate insulating film; a conductive polymer layer disposed to cover at least a portion of each of source and drain electrodes; a hydrophobic material layer disposed on the substrate and the source and drain electrodes except regions where the conductive polymer layer are formed; an organic semiconductor layer electrically connected to the source and drain electrodes; a gate insulating film disposed to cover the organic semiconductor layer; and a gate electrode disposed on the gate insulating film.