A device for automatically aligning bipolar electrodes on opposing sides of operative tissue is provided for performing minimally invasive RF ablation. The device includes complementary magnetic electrode assemblies, each having a permanent magnet mechanically coupled to and electrically insulated from an electrical conductor. When positioned on opposing sides of tissue such as an atrial wall, the complementary assemblies automatically align their respective electrical conductors through mutual magnetic attraction to complete an electrical circuit. Each electrical conductor may provide an alignable elongated transmitting element adjacent to a magnetic coupling surface to allow for ablation of linear segments of tissue. Each electrode assembly includes mechanical linkage for coupling to an intracorporeal positioning device and a wire receiving terminal for connection to an external generator.
