The understanding of the interactions between biological systems and nanoengineered devices is crucial in several research fields, including tissue engineering, biomechanics, synthetic biology and biomedical devices. This review discusses the current knowledge of the interactions between bacteria and abiotic nanostructured substrates. First, the effects of randomly organized nanoscale topography on bacterial adhesion and persistence are described. Second, the interactions between microorganisms and highly organized/ordered micro- and nano-patterns are discussed. Finally, we survey the most promising approaches for the fabrication of silver polymeric nanocomposites, which have important applications as antimicrobial materials. The advantages, drawbacks and limitations of such nanotechnologies are critically discussed in view of potential future applications.