Our understanding of basic cell structure and function has been greatly aided by the identification of proteins at the ultrastructural level. However, the current methods for high-resolution labeling of proteins in situ, and for directly correlating observations made by light microscopy (LM) and electron microscopy (EM) although invaluable, have a number of substantial limitations. These range from poor label penetration, difficulty to perform simultaneous multiprotein labeling, or the need to take the samples all the way to the electron microscope to evaluate labeling efficacy. Here we demonstrate an approach using quantum dots for pre-embedding immunolabeling of multiple diverse proteins for both LM and EM that overcomes many of these problems.