Crystalline bacterial cell surface layers (S-layers) composed of identical protein units have been used as binding templates for well-organized arrangements of nanoparticles. Isolated S-layer proteins were recrystallized into monomolecular arrays on solid substrates (such as silicon wafers and SiO2-coated grids) and in suspension forming so-called self-assembly products. These S-layer assemblies were studied by atomic force microscopy and transmission electron microscopy (TEM). The orientation of the S-layer lattice, exhibiting anisotropic surface properties, on the solid surface and on the self-assembly products, was compared with the orientation on the bacterial cell. On both bacterial cells and SiO2 surfaces the outer face of the S-layer protein was exposed. On the self-assembly products occasionally the inner face was also visible. Metal- and semiconductor nanoparticles 2 to 10 nm in mean diameter were covalently or electrostatically bound to the solid-supported S-layers and self-assembly products. TEM studies reveal that upon activation of carboxyl groups in the S-layer lattice with 1-ethyl-3,3'(dimethylaminopropyl)carbodiimide (EDC), a close-packed monolayer of 4-nm amino-functionalized CdSe nanoparticles could be covalently established on the S-layer lattice. Because of electrostatic interactions, anionic citrate-stabilized Au nanoparticles (5 nm in diameter) formed a superlattice at those sites where the inner face of the S-layer lattice was exposed. In contrast, cationic semiconductor nanoparticles (such as amino-functionalized CdSe particles) formed arrays on the outer face of the solid-supported S-layer lattices.