During the symposium on surrogate markers of HIV, the Scientific Advisory Committee posed the following question: "Which surrogate markers currently deserve the greatest commitment of investigative resources to validate them in a clinical setting?" The Committee concluded that for antiretroviral drugs measurements of HIV RNA in plasma deserve the greatest priority, and for immune-based therapies assessing viral load still had the highest priority. But it was recognized that assessing viral load should not be restricted to plasma RNA because the primary mechanisms of action are different from antiretroviral drugs. Thus, the Committee voted that based on current knowledge, investigating the clinical relevance of changes in HIV-1 DNA and RNA copy number in peripheral blood mononuclear cells (PBMCs) with validated assays should be given equal focus for immune-based therapies. This article reviews the rationale for using HIV-1 DNA and RNA load in PBMCs for the monitoring of clinical trials and presents recent data that indicate that the postseroconversion level and the dissemination of proviral DNA in the blood cells have prognostic value, i.e., high levels correlate with disease progression. In addition, longitudinal studies show that an increase in proviral DNA and/or HIV mRNA load correlates with disease progression. We present evidence that these markers are relevant activity markers for anti-HIV therapies. Changes in both DNA and RNA load can be achieved using either antiretroviral drugs or immune-based therapies. These results suggest that these markers should be evaluated in clinical studies to firmly establish their value as surrogates of clinical progression.