Two-dimensional bacterial cell surface layer protein crystals (S-layers) are the most commonly observed cell surface structure in bacteria and archaea. Isolated S-layer proteins have the intrinsic tendency to self-assemble into crystalline arrays in suspension and on various interfaces. Basic research on the structure, genetics, chemistry, morphogenesis and function of S-layers has led to a broad spectrum of applications in nanotechnology and biomimetics. The possibility to change the properties of S-layer proteins by genetic engineering opens new ways for tuning their functional and structural features. Functionalized S-layer proteins that maintain their ability to self-assemble have led to new affinity matrices, diagnostic tools, vaccines or biocompatible surfaces, as well as to biological templating or specific biomineralisation strategies at surfaces.