For over three decades, bacteriorhodopsin has served as a paradigm for the study of the mechanisms underlying ion pumping across biological membranes. It is perhaps among the simplest known ion pumps, which functions by converting light energy into an electrochemical gradient by pumping protons out of the cytoplasm. The combination of spectroscopic, biochemical and crystallographic studies on bacteriorhodopsin provides a unique opportunity to dissect the principal elements underlying the mechanism of transmembrane proton transport. Here, we provide a brief review of recent developments related to the determination of the structural changes during proton transport using crystallographic approaches. Taken together with previous spectroscopic and biochemical investigations, these studies allow the description of a detailed molecular mechanism of the main steps in vectorial proton transport by bacteriorhodopsin.