A system has been developed to measure the molecular weights of macromolecular assemblies using low-dose, dark-field, high resolution scanning transmission electron microscopy (STEM) . Mass maps were obtained from a number of test samples including tobacco mosaic virus and limpet hemocyanin. Measurements were also made on brain microtubules and on the microtubule-associated protein, kinesin ATP-ase, the motor protein for anterograde axonal transport.