COBAS TaqMan assay is a new HIV assay for measuring plasma viral load (VL). A significant number of patients with undetectable plasma VL on Amplicor assay were reported to have detectable VL with TaqMan in the study centre. The aim of the present study was to investigate the significance of detectable VL counts with TaqMan assay amongst patients who have had undetectable plasma VL with COBAS Amplicor assay. Observational study on patients who have had undetectable (40 copies/mL) in 113 (14%) patients on 126 episodes using TaqMan assay. VL was less than 500 copies/mL in 90% of those episodes. All episodes ended with VL <40 copies/mL after a median of 117 (94-143) days without change in HAART regimes. The duration of those episodes was longer than 150 days in 75% of cases. No new mutation was detected amongst specimens with detectable VL. Short-term detectable VL may be common with using TaqMan assay. This phenomenon did not result in new mutations or failure of HAART in study patients in the short term.