The presence of HIV-1 RNA in distal duodenal mucosa was evaluated in 44 HIV-1-positive patients. HIV-1 RNA was detected in gut tissue in antiretroviral-naive patients with high plasma viral loads, as well as in patients on HAART with plasma viral loads below the limit of detection and in patients on HAART with virological failure. The intestinal mucosa seems to serve as a reservoir poorly influenced by levels of plasma viral load or HAART.