The outermost component of many bacterial cell envelopes is a two-dimensional crystalline array of protein molecules, termed the S-layer1. Despite considerable effort to investigate its structure and composition, its precise function remains uncertain. We report here the first determination of the three-dimensional structure of an S-layer, that from the thermophilic bacterium, Sulfolobus acidocaldarius. Our map shows a complex and strongly interconnected structure, penetrated by numerous channels which appear to provide little barrier to anything but rather large molecules. The external surface is fairly smooth, but the cellular side is sculpted with large cavities and protruding ‘pedestals’. The protein substructure consists of three types of globular domain, connected by narrow bridges. We suggest that these may be flexible ‘hinges’, allowing the S-layer to form a curved surface, and that the multidomain structure allows the S-layer to maintain strong connectivity as it grows with the bacterium.