This work describes the development of a fully polymeric microchip with integrated polymeric electrodes suitable for performing microchip electrophoresis. The polymer electrodes were fabricated in a thin film of the conducting polymer, polyaniline (PANI), by flash lithography using a studio camera flash and a transparency mask. During flash welding, exposed regions welded into non-conducting regions forming a conducting polymer circuit in the non-exposed regions. Using a structured layer of dry film photoresist for sealing, a polydimethylsiloxane (PDMS) substrate containing channels and reservoirs was bound to the PANI film to form an integrated microfluidic device. The conducting regions of the PANI film were shown to be capable of carrying the high voltages of up to 2000 V required for chip electrophoresis, and were stable for up to 30 minutes under these conditions. The PANI electrodes were used for the electrophoretic separation of three sugars labelled with 8-amino-1,3,6-pyrenetrisulfonic acid (APTS) in the dry film resist—PDMS hybrid device. Highly efficient separations comparable to those achieved in similar microchips using platinum electrodes confirm the potential of polyaniline as a new material suitable for high voltage electrodes in Lab-on-a-chip devices.