BACKGROUND Anti-retroviral drug therapy reduces but does not abolish HIV transmission and replication throughout the body. HIV DNA 2-long terminal repeat (2-LTR) circles have been shown in point-based studies to persist in some patients whose plasma HIV RNA was undetectable. However, the degree of fluctuation of circle copy number over time has not been determined. METHODS A reliable, reproducible and robust quantitative LightCycler (LC qPCR)-based assay for HIV DNA 2-LTR circles in peripheral blood mononuclear (PBMN) cells was established. A prospective, longitudinal study of these circles was undertaken in HIV-1-positive patients on anti-retroviral therapy whose plasma HIV RNA was undetectable at < 50 copies/ml. Patients starting therapy for the first time were also monitored. RESULTS A cohort of 60 patients whose plasma HIV RNA was undetectable for 32 +/- 2 months were monitored for circles for 15 +/- 2 months. The circle copy number ranged from < 10 to 620 copies/106 PBMN cells. The circle-negative (< 10 copies/1 x 106 PBMN) cells group of 36 patients and the circle-positive (> 10 copies/106 PBMN cells) group of 24 patients were mutually exclusive (P < 0.0001). The mean circle half-life in seven of the 10 patients starting anti-retroviral therapy for the first time was 5.7 days. CONCLUSION The circle assay is useful for identifying those patients in whom transmission of infectious virus continues despite prolonged periods of time during which plasma HIV RNA is undetectable. New drug combinations and new therapeutic approaches should be aimed at those patients whose plasma HIV RNA is undetectable but who remain positive for 2-LTR circles.