Cellular phenotyping of immune cells is a critical component of understanding the immunological impact of Marburg virus on the host. Moreover, it is also important to identify correlates of protection in vaccine or therapeutic preclinical and clinical studies. The protocol below describes the isolation and storage of peripheral blood mononuclear cells, proper thawing techniques, cellular stimulation guidelines, and extracellular and intracellular flow cytometry staining used to obtain cellular phenotyping data. This protocol allows for the detection and characterization of cellular phenotypes as well as their activation states. The potential of this protocol for the detailed characterization of the cellular response is limited by the researcher’s interest and the capabilities of the flow cytometer available for use. Hence, this protocol may be used as a starting point and fine-tuned to the researcher’s own interests.