OBJECTIVE:: Residual immune activation and skewed T cell maturation may contribute to excess comorbidity and mortality in successfully treated HIV infected patients and long term effects of combination antiretroviral therapy (cART) on immune reconstitution remain a debated issue. We investigated quantitative T cell reconstitution and activation and its association to residual viraemia in patients with 12 years of viraemic suppression. DESIGN:: Blood samples collected cross-sectionally from 71 HIV infected patients with cART induced viraemic suppression through 12 years were compared to samples from 16 healthy controls. METHODS:: Several different subsets of naïve, memory and activated T cells were analyzed in fresh whole blood by 6-color flowcytometry and ultra sensitive quantification of HIV RNA was performed. RESULTS:: HIV-infected patients (HIV+) had lower absolute and relative CD4 T cell counts and higher absolute and relative CD8 T cell counts than controls. HIV+ had lower concentrations of naïve CD4 cells than controls, but proportions were similar. HIV+ had higher concentrations of CD8+ T cells than controls in all of the examined subsets, but only a higher proportion of CD8+ cells in the intermediately differentiated and activated subsets. Residual viraemia did not correlate to proportions of naïve CD4, CD4 RTEs, or activated CD8 T cells. CONCLUSIONS:: This study demonstrated some degree of T cell imbalance even after 12 years of successful cART. Large longitudinal studies are needed to establish whether or not these discrete changes have clinical relevance.