HIV cure efforts are hampered by limited characterization of the cells supporting HIV replication in vivo and inadequate methods for quantifying the latent viral reservoir in patients receiving antiretroviral therapy. We combine fluorescent in situ RNA hybridization with detection of HIV protein and flow cytometry, enabling detection of 0.5–1 gag-pol mRNA+/Gag protein+-infected cells per million. In the peripheral blood of untreated persons, active HIV replication correlated with viremia and occurred in CD4 T cells expressing T follicular helper cell markers and inhibitory co-receptors. In virally suppressed subjects, the approach identified latently infected cells capable of producing HIV mRNA and protein after stimulation with PMA/ionomycin and latency-reversing agents (LRAs). While ingenol-induced reactivation mirrored the effector and central/transitional memory CD4 T cell contribution to the pool of integrated HIV DNA, bryostatin-induced reactivation occurred predominantly in cells expressing effector memory markers. This indicates that CD4 T cell differentiation status differentially affects LRA effectiveness. Display omitted •HIV RNA and protein co-expression allows ex vivo characterization of patient CD4 T cells•HIV-infected CD4s show markers of exhaustion and peripheral follicular helper cells•Translation-competent latent reservoir can be detected in most ART-treated patients•PKC agonist Bryostatin preferentially reactivates HIV from effector memory CD4s Technological limitations hamper characterization of CD4 T cells supporting ongoing HIV infection and quantification of the latent reservoir. Baxter et al. (2016) use simultaneous detection of viral protein and mRNA to quantify and phenotype both the ongoing infection during viremia and the translation-competent inducible reservoir in virally supressed, treated patients.