We investigated the relationship between viral persistence in the gut, microbial translocation, and T cell activation during chronic HIV infection. Plasma levels of LPS, fraction of circulating CD8+CD38+ T cells, and levels of HIV-DNA in rectosigmoid biopsies and peripheral blood mononuclear cells were determined in 22 HIV-infected individuals and 10 healthy controls. We found that in untreated HIV-infected individuals, HIV-DNA load was higher in the gut mucosa than in the blood. Also, ART-treated patients exhibited lower levels of LPS and CD8+CD38+ T cells than untreated patients, but higher levels than controls. In ART-treated individuals, the level of HIV-DNA in the gut correlated with levels of LPS and fraction of CD8+CD38+ T cells. We concluded that in ART-treated individuals, higher levels of gut-associated HIV-DNA are associated with persistent immune activation and microbial translocation.