Considerable attention has been focused on CD8 and CD4 T cell responses as a major element of the cellular immune response to viral infections including human immunodeficiency virus (HIV) and hepatitis C virus (HCV). However, increasing evidence based on the recent introduction of more quantitative assays for measuring antigen-specific T cells has suggested that the role of these cells in the development of a protective immune response to a particular viral pathogen may be determined by a complex interplay of multiple virologic and cellular factors. Thus, measurements of only the frequencies of the T cell subsets participating in the response to viral pathogens may be an incomplete reflection of efficacy. In this review, we suggest that some measurable factors may influence the role of T cell immunity in conferring protection, including functional avidity, epitope breadth and specificity, proliferative capacity, cytokine repertoire, degree of anergy, and differentiation phenotype, as well as magnitude, of viral-specific CD4 and CD8 T cells. We suggest that automated cytokine flow cytometry (CFC) is an efficient approach to the measurement of the complex interplay of multiple immune parameters involved in immune protection. These ideas are discussed in the context of new developments in sample preparation and analysis automation.