Despite undetectable viral load in conventional assays, probably all human immunodeficiency virus (HIV)-1 infected patients have residual viraemia (RV) detectable by ultra-sensitive assays. To study this issue, this study investigated virologic and immunologic consequences of RV in highly active antiretroviral therapy (HAART)-treated HIV-1-infected patients with plasma HIV-1 RNA ≤20 copies/ml. The study included 32 HAART-treated HIV-1-infected patients with HIV-1 RNA ≤20 copies/ml followed prospectively 6-monthly for 24 months. RV was detected by transcription-mediated amplification (TMA-RV) technique (Procleix® HIV-1 Discriminatory Assay; Chiron) and by PCR (PCR-RV, Amplicor HIV-1 Monitor Assay; Roche Diagnostics). The association between RV and proviral-HIV-1-DNA, CD4-count, CD8-count, soluble [soluble tumour necrosis factor receptor (TNFr)-II, β2-microglobulin, immunoglobulins] and cellular (HLA-DR, CD38, CD45RO, CD45RA, CD62L) T-cell markers of immune activation was investigated. In the 24-months study-period, 23 patients had ≥1 episode with TMA-RV whereas 9 patients had undetectable TMA-RV throughout the study-period. Time-points with TMA-RV and PCR-RV were associated with higher circulating sTNFrII (+0.234 ng/ml, P = 0.030) and β2-microglobulin (+22 nmol/l, P = 0.016) and time-points with PCR-RV were also associated with higher IgA (+0.82 μmol/l, P = 0.035) and CD8-count (+1.18-fold, P = 0.001). Patients with TMA-RV in the study-period had higher HIV-1 RNA pre-HAART (P = 0.032). RV was not associated with proviral-HIV-1-DNA, CD4-count, CD4+HLA-DR+, CD8+HLA-DR+CD38+, CD4+CD45RA−CD45RO+, CD8+CD45RA−CD45RO+, CD4+CD45RA+CD62L+, CD8+CD45RA+CD62L+ T cells, IgG or IgM. In conclusion, RV was associated with increased blood levels of soluble immune activation markers in HAART-treated HIV-1-infected patients. The finding that RV was associated with higher pre-HAART plasma viral load suggests that RV is linked to pre-HAART disease progression.