A conductivity measurement system measures conductivity of molecules. A substance to be measured is applied to the first and second electrodes. A potential is applied across the electrodes. A computer-controlled motion controller moves a first electrode relative to a second electrode in discrete steps. In a first step, the electrodes are brought together in physical contact to form a plurality of molecular junctions. The electrodes are separated by a first distance which breaks a first molecular junction. The electrodes are separated by a second distance which breaks a second molecular junction. A conductivity measure is taken at each step. The process of separating the electrodes continues until conductivity measure is zero. The conductivity of one molecule corresponds to a last non-zero conductivity measurement prior to a zero conductivity measurement.