Multiplex immunofluorescence (IF) utilizes a combination of different fluorophore-linked antibodies to facilitate the simultaneous observation of multiple antigenic epitopes within a tissue section. In this chapter, we describe how tick-borne flaviviruses can be visualized in mouse skin biopsies harvested from the tick feeding site or in mouse brain tissue. Using antibodies specific to the North American tick-borne flavivirus, Powassan virus (POWV), and to Mus musculus cell markers, IF multiplex labeling experiments allow us to visualize how POWV antigen co-localizes with host cell markers. Such IF multiplexing in mouse skin and brain tissue suggests which host cells are targets of viral infection.