We present the first detailed report that directly correlates the reduced contact resistance in organic thin-film transistors (TFTs) with fundamental structural and morphological characterization at the organic semiconductor/conducting polymer interface. Specifically, the pentacene grains are similar in size and continuous across the channel/electrode interface in bottom-contact TFTs with polyaniline (PANI) electrodes. On a molecular level, the fused rings of pentacene are oriented perpendicular to the surface both in the channel and on PANI. Accordingly, the contact resistance is small in such devices. In TFTs with gold electrodes, however, the pentacene grains are different in size and are discontinuous across the channel/electrode interface. Further, the fused rings of pentacene are oriented perpendicular to the channel surface and parallel to the gold surface. Such differences across the channel/electrode interface lead to structural and electronic disorder, which manifests itself as a significantly larger contact resistance in devices with gold electrodes.