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Most of the body's lymphoid tissue is in gut and constitutes an immense HIV reservoir. We quantified HIV-DNA in rectum and compared it with blood levels for 27 HIV-infected adults from different groups. We observed a large range of rectal and blood HIV-DNA levels. They were positively correlated (r = 0.841, P < 0.0001). Long-term nonprogressors and patients in ‘remission’ after antiretroviral treatment interruption had the lowest blood and mucosal HIV-DNA levels.