Over the last years, a paradigm shift has occurred from approaching viruses solely as disease-bringing agents toward regarding them as functional nanoparticles, and a perfect example of Nature's capability to self-assemble complex, multicomponent materials at the nanoscale. Viruses are now used as templates for constructing specific nanocontainers, either by changing the properties of the viruses themselves or by copying their compact, shelled structure into engineered materials, which are able to encapsulate various agents. To exploit the mechanisms used by nature to create functional nanocontainers, we need to understand what their material and biomechanical properties are. Nanoindentation, a technique based on atomic force microscopy, is perfectly suited to determine these characteristics. Here, we discuss the advances this research field has achieved, exploring prokaryotic (bacteriophages) as well as eukaryotic viruses. The material properties of viral shells (capsids) and of more complex viral assemblies are analyzed and compared. We discuss the Young's modulus of capsids, the maximal forces viruses can withstand, and explore the occurrence of material fatigue in nanosize objects. Finally, the impact of internalized materials and of specific alterations to the capsid proteins on the particle's mechanical strength is analyzed. © 2009 WILEY-VCH Verlag GmbH & Co. KGaA.