The cross-fertilization of biology, chemistry, material sciences, and solid-state physics is opening up a great variety of new opportunities for innovation in nanosciences. One of the key challenges is the technological utilization of self-assembly systems wherein molecules spontaneously associate under equilibrium conditions into reproducible supramolecular aggregates. The attractiveness of such processes lies in their capability to build uniform, ultrasmall functional units and the possibility of exploiting such structures at meso- and macroscopic scale for life and nonlife science applications. The use of crystalline bacterial cell-surface proteins (S-layer proteins) provided innovative approaches for the assembly of supramolecular structures and devices with dimensions of a few to tens of nanometers. S-layers have proven to be particularly suited as building blocks in a molecular construction kit involving all major classes of biological molecules. The immobilization of biomolecules in an ordered fashion on solid substrates and their controlled confinement in definite areas of nanometer dimensions are key requirements for many applications including the development of bioanalytical sensors, biochips, molecular electronics, biocompatible surfaces, and signal processing among functional membranes, cells, and integrated circuits.