The plasma membrane is made up of a complex mosaic of different functional microdomains, but the tools required to accurately visualize them have always been limited. We present a protocol that allows both inner and outer leaflet domains to be visualized on a nanometer scale. With a combination of electron microscopic and statistical analysis approaches, it is possible to screen proteins associating with, and co-localizing within, lipid rafts and other morphologically featureless microdomains. The approach has enormous potential to determine plasma membrane organization and the spatial dynamics of regulated signaling and membrane trafficking events associated with the cell surface.