Flow cytometry is a multiparameter single-cell assay ubiquitous in HIV/AIDS clinical and research settings for evaluating the immune response to the virus, therapy, and vaccination. In clinical practice, flow cytometry is used to monitor the CD4 and CD8 T cell counts of HIV-infected subjects. In research settings, flow cytometry is used to evaluate innate and antigen-specific responses to the HIV virus, so as to better understand pathogenesis, the mechanisms responsible for long-term nonprogression, and to develop effective immune-based interventions. In vaccine development, there is significant interest in the potential of flow-based biomarkers that can serve as surrogate measures of efficacy.