Objective: To assess the prognostic significance of persistent low-level viraemia (PLV, defined as persistent plasma viral loads of 51-1000 HIV-1 RNA copies/mL for at least 3 months) in patients who had achieved viral suppression on antiretroviral therapy (ART). Methods: A retrospective cohort of HIV-infected patients who received ART, were followed-up for ≥12 months, made regular visits to the clinic during which blood tests were performed for an ultrasensitive HIV RNA assay every 3 months, and achieved viral loads <50copies/mL were evaluated. Virological failure was defined as two consecutive viral load measurements >1000copies/mL. Results: Of 362 patients, 78 (27.5%) experienced PLV. The demographics of patients with and without PLV were similar. PLV occurred at a mean (±standard deviation) of 22.6±16.9 months after ART initiation and lasted for 6.4±3.4 months. During a median follow-up of 29.5 months, patients with PLV had a higher rate of virological failure (39.7%; vs 9.2%; P <0.001). The median time to failure was 68.4 months [95% confidence interval (CI) 37.0-99.7] for patients with PLV and >72 months for patients without PLV (log rank test, P <0.001). By Cox regression, patients with PLV had a greater risk of virological failure [hazard ratio (HR) 3.8; 95% CI 2.2-6.4; P <0.001]. Among patients with PLV, a PLV of >400copies/mL (HR 3.3; 95% CI 1.5-7.1; P =0.003) and a history of ART (HR 2.4; 95% CI 1.0-5.7; P =0.042) predicted virological failure. Conclusions: PLV is associated with virological failure. Patients with a PLV >400copies/mL and a history of ART experience are more likely to experience virological failure. Patients with PLV should be considered for treatment optimization and interventional studies. © 2006 British HIV Association.