A nanoimprinting process that enables fabrication of self-aligned p-and n-type organic thin film transistors with small channel lengths is presented. Nanoimprint lithography with back-side exposure permit precise definition of the channel length down to the sub-micrometer regime and a diminutive gate to source/drain overlap. The self-aligned manufacturing process enables transistor setups with minimized electrode overlaps resulting in distinct decrease of parasitic capacitances and considerable increase in transition frequency. Fully functional small channel OTFTs with p- and n-type semiconductors are fabricated on glass as well as on flexible substrates with transition frequencies up to 400 kHz.