Nanoindentation is a valuable tool for mapping mechanical properties in samples from small animal models and can aid in generation of structure-property relationships in hierarchical biological materials at some of their smallest length scales, which can have important applications in clinical medicine and materials development. Although a young field, nanoindentation has been applied to studies of diverse biological materials. This chapter will focus primarily on soft tissue characterization using nanoindentation, with an emphasis on cartilage studies, but will also briefly review the application of nanoindentation techniques to other non-mineralized biological materials such as wood, plant leaves, and spider silk to highlight the broad range of research questions that can be addressed using this high resolution mechanical characterization tool. The challenges that are faced in adapting the nanoindentation technique to the study of compliant, hydrated soft tissues will also be discussed, and some of the current approaches to overcoming those challenges will be summarized.