The ultrasensitive COBAS AMPLICOR HIV-1 Monitor test was complemented with automated RNA purification on the MagNA Pure LC instrument. This enabled entirely automated ultrasensitive assessment of viral loads in human immunodeficiency virus type 1 (HIV-1)-infected individuals. The detection limit of the fully automated assay and the viral load measurements in 80 clinical samples were found to be in good agreement with those of the conventional ultrasensitive COBAS AMPLICOR HIV-1 Monitor test. The fully automated assay showed markedly reduced hands-on time and was found to be suitable for the routine assessment of HIV-1 viral loads in a clinical diagnostic laboratory.