This chapter provides an example of the use of electron crystallography in the high-resolution structure analysis of a membrane protein. Bacteriorhodopsin (bR) is a light-driven proton pump found in the membrane of Halobacterium salinarium. Many high-resolution images and electron diffraction patterns of specimens have to be recorded at various tilt angles with minimal electron exposure. Two-dimensional (2D) crystallization currently constitutes the bottleneck for the electron crystallographic structure analysis of membrane proteins. 2D crystals suitable for high-resolution electron crystallography are normally grown from detergent-solubilized and extensively purified membrane proteins. Since electron crystallography can discriminate between the charged and uncharged states of the key amino acid residues in the transmembrane helices of bR based on the characteristic difference of the electron scattering factors, would be able to follow the proton on its passage through the bR channel.