The role of Epstein-Barr virus (EBV) lytic cycle gene expression in lymphocytes in the pathogenesis of EBV-associated diseases is incompletely understood. The ability to physically separate lytically induced from latently infected cells from the same population and to examine them in parallel would significantly enhance understanding of the viral, cellular, and environmental factors that govern susceptibility of an EBV-infected cell to lytic cycle induction stimuli at the single cell level. This study demonstrates, using a flow cytometry-based system, that human serum immunoglobulins from individuals immune to EBV reproducibly discriminate between and can be used to physically separate lytically induced from latently infected B cells. Using this new quantitative and sensitive technique, two novel observations about lytic cycle activation were made. First, the kinetics of lytic cycle activation by histone deacetylase inhibitors is more rapid than induction by a DNA methyl transferase inhibitor. Second, butyrate-treated cells which are initially refractory to lytic cycle activation can be induced upon subsequent exposure to the inducing agent. Therefore, susceptibility to lytic cycle induction of a latently infected B cell is governed by environmental and physiologic factors and not by permanent cellular or viral genetic changes.