The cobas 5800 System ("cobas 5800") is a new low- to mid-throughput PCR-based nucleic acid testing system which performs both qualitative and quantitative testing, including viral load (VL) determination. cobas 5800 shares numerous design elements and technical characteristics with the existing cobas 6800/8800 Systems. We compared HBV, HCV, and HIV-1 VL results from cobas 5800 in three different laboratories to those from the same specimens tested on a cobas 6800 system. We also assessed cobas 5800 assay reproducibility by repetitive testing of specimens with VL close to values used as thresholds for patient management or classification. The correlation between VL measurements generated using cobas 5800 versus 6800 was extremely high, with r correlation coefficients between 0.990 and 0.999 for the three targets at the different sites. The slope of the Deming regression line ranged from 0.994 (HBV, site 3) to 1.025 (HIV-1, site 1). The standard deviation values ranged from 0.04 to 0.19 log IU/mL for HBV, 0.06 to 0.33 log IU/mL for HCV, and 0.05 to 0.34 log copies/mL for HIV-1. In general, variability was higher at lower VL. Between 98.6% and 100% of results fell within the allowable total difference zone that defines expected variability on the existing 6800/8800 system. This multisite comparison study demonstrates equivalent performance of the new cobas 5800 system compared with cobas 6800. This establishes cobas 5800 as a new option for low- to mid-throughout laboratories seeking to optimize efficiency of their viral molecular testing. These are the first published data that demonstrate equivalent performance of the new cobas 5800 system compared with cobas 6800. This fulfills an unmet need for low- to mid-throughout laboratories seeking to optimize efficiency of their viral molecular testing.