Natural killer (NK) cells play a critical role in defending against virus infections. Investigating human NK cell antiviral functions is of prime importance; however, there are challenges such as the human-specific nature of many viruses and differences in NK cell surface markers between humans and rodents. Research on the antivirus response of human NK cells must therefore be carefully planned around species tropism of the viruses of interest and the specific biological questions to be answered. The initial site of many virus infections is a mucosal/epithelial surface. In this context, a clinical virus infection at the ocular surface enables direct analyses on the mechanisms and consequences of infection and immune reactions in situ over the course of disease. For example, the site of infection of a clinical infection in the conjunctiva and cornea can be directly observed in real-time, utilizing split-lamp microscopy, and specimens are readily accessed with minimally invasive techniques. In this chapter, we describe protocols for investigating NK cell responses using clinically isolated viruses in co-culture assays. We also describe procedures for ex vivo analysis of conjunctiva-derived NK cells in adenovirus infection.