We developed a procedure for fabricating sub-1 nm gap Au electrodes using a metal mask for electrode patterning. Self-aligned nanogap formation was achieved using an electromigration method during metal deposition. We also measured the electric conductivities of organic molecules using the new nanogap electrodes. Because the new procedure does not involve wet processing, the ranges of possible electrode and substrate materials for the nanogap electrodes are greatly expanded. Finally, we discussed the molecular orbital energies of bridging and nonbridging 1,4-benzenedithiol molecules between Au electrodes. The new procedure for the fabrication of nanogap electrodes is expected to be useful for measuring the electrical properties of various nanoscale materials.