An organic thin film transistor (TFT), a method of manufacturing the organic TFT, and a flat display apparatus having the organic TFT are provided. The organic TFT has a gate insulating layer with openings filled with a conductive material, thereby preventing short circuits from occurring between channels connecting the source and drain lines to the organic semiconductor layer. The organic TFT includes a substrate including a source line, a drain line, and a gate electrode. The organic TFT further includes a gate insulating layer formed on the source and drain lines and on the gate electrode. The gate insulating layer has openings exposing the source and drain lines, which openings are filled with a conductive material. The organic TFT also includes an organic semiconductor layer electrically connected to the conductive material.