Research suggests that some low-level virological rebound results occurring for no obvious clinical cause, in patients stable on antiretroviral treatment, may be a consequence of the viral load assay used. We compared the relative frequency of clinically unexplained low-level virological rebound results when using the Roche HIV Taqman version-1 (CTM v1), the Roche HIV Taqman version-2 (CTM v2) and the Abbott RealTime (Abbott RT) assay in clinical practice. In all, 247 patients from our centre who had their viral loads measured by the three different assays over a period of 3 consecutive years (each assay used for a period of 1 year each) were included in the study. Low-level virological rebound was defined as <1000 copies/ml. Over similar time periods, there was significant discrepancy between the three assays when considering the proportion of clinically unexplained low-level virological rebound results in patients stable on ARVs: CTM v2 assay producing the highest percentage (93%), CTM v1 much lower (65%) and Abbott RT even less (35%). There is further research required regarding what, if any, implications this has for patients having the clinically unexplained low-level virological rebound on the more sensitive assays.