bQuantification of HIV-1 RNA has become the standard of care in the clinical management of HIV-1-infected individuals. The objective of this study was to evaluate performance characteristics and relative workflow of the Aptima HIV-1 Quant Dx assay in comparison with the Abbott RealTime HIV-1 assay using plasma and cervicovaginal lavage (CVL) specimens. Assay performance was evaluated by using an AcroMetrix HIV-1 panel, AcroMetrix positive controls, Qnostics and SeraCare HIV-1 evaluation panels, 208 clinical plasma samples, and 205 matched CVL specimens on the Panther and m2000 platforms. The Aptima assay demonstrated good linearity over the quantification range tested (2 to 5 log 10 copies/ml), and there was strong linear correlation between the assays (R 2 ؍ 0.99), with a comparable coefficient of variance of <5.5%. For the plasma samples, Deming regression analyses and Bland-Altman plots showed excellent agreement between the assays, with an interassay concordance of 91.35% (kappa ؍ 0.75; 95% confidence interval [CI], 0.65 to 0.85), and on average, the viral loads determined by the Aptima assay were 0.21 log 10 copies/ml higher than those determined by the RealTime assay. The assays differed in their sensitivity for quantifying HIV-1 RNA loads in CVL samples, with the Aptima and RealTime assays detecting 30% and 20%, respectively. Aptima had fewer invalid results, and on average, the viral loads in CVL samples quantified by the Aptima assay were 0.072 log 10 copies/ml higher than those of the RealTime assay. Our results demonstrate that the Aptima assay is sensitive and accurate in quantifying viral loads in both plasma and CVL specimens and that the fully automated Panther system has all the necessary features suitable for clinical laboratories demanding high-throughput sample processing. Q uantitation of HIV-1 RNA has been an established surrogate marker for monitoring viral suppression and drug efficacy during antiretroviral therapy (ART) in HIV-infected patients. Early diagnosis during the acute phase of infection represents a tremendous opportunity for treatment and prevention interventions, as the HIV-1 concentration in both plasma and genital fluids is intensely high during this phase (1, 2). It is apparent from previous studies that plasma viral load has been an important determinant in detecting HIV-1 in the genital tract (3-5). RNA levels in cervicovaginal lavage (CVL) specimens are usually lower than plasma HIV-1 RNA loads; thus, HIV-1 RNA suppression in the genital tract may occur more rapidly than in plasma after initiation of therapy (6). Nevertheless, more recent studies demonstrate that genital HIV-1 RNA shedding occurs in women on highly active antiretroviral therapy (HAART) even in the absence of plasma viremia (7,8). Therefore, an HIV-1 assay that accurately quantifies both genital and plasma RNA levels is a powerful research tool to better understand HIV-1 pathogenesis in the genital tract. Measurement of HIV-1 loads in CVL samples is challenging due to the presence of inhibitors of amp...