The degree of infection of memory and naive CD4⁺ T cells in patients treated with HAART and with durable undetectable or detectable viral load in plasma was evaluated. The following two groups of patients were analyzed cross-sectionally: (i) patients with undetectable HIV RNA plasma levels during follow-up (responders); (ii) patients with no reduction or with rebound in HIV RNA levels during treatment (non-responders). Patients were examined following 6,12,18 and 24 months of HAART, respectively, by quantifying: (i) plasma HIV RNA load; (ii) CD4⁺ T cells; (iii) memory and naive CD4⁺ T cells; (iv) HIV DNA levels in memory and naive CD4⁺ T cells. HIV RNA plasma levels were significantly higher in non-responders vs responders at each time point (P<0.02), while CD4⁺ T cell counts as well as memory and naive CD4⁺ T cell levels were comparable in both viremic and non-viremic patients. However, higher HIV DNA values were observed in both memory and naive CD4⁺ T cells of non-responders vs responders after 18 and 24 months of HAART (P<0.02), suggesting an increased amount of HIV-infected naive CD4⁺ T cells and a sustained high degree of infection of memory CD4⁺ T cells. Immunological reconstitution following HAART might potentially be hampered in viremic patients despite the absolute increase in CD4⁺ T cell counts.