The increasing emergence of multiple-drug-resistant pathogens has made the search for alternatives to traditional antibiotics a high priority. Likewise, more rapid and sensitive methods for the detection and prevention of microbial infections are in constant demand in the clinical and environmental fields. Nanotechnology offers new solutions to these problems. Nanoparticles and nanotubes, along with other nanoscale materials, either in inorganic format (such as metallic nano-particles, carbon nanotubes) or biofunctionalized with biomolecules (antibodies, carbohydrates, or antibiotics) have found applications as antibacterial, antifungal, and antiviral agents. Using various biofunctionalized nanomaterials, techniques have also been developed for rapid and sensitive detection, capture and/or separation of pathogens. Some of the recent scientific reports exemplify the achievements in this field. Here we review progress in the use of nanomaterials as alternatives to classical antibiotic therapy and as agents for the rapid and sensitive detection of pathogens in mixed microbial populations.