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HIV persists in tissues during antiretroviral therapy (ART), but the relative contribution of different anatomical compartments to the viral reservoir in humans remains unknown. We performed an extensive characterization of HIV reservoirs in two men who donated their bodies to HIV cure research and who had been on suppressive ART for years. HIV DNA is detected in all tissues, with large variations across anatomical compartments and between participants. Intact HIV genomes represent 2% and 25% of all proviruses in the two participants and are mainly detected in secondary lymphoid organs, with the spleen and mediastinal lymph nodes harboring intact viral genomes in both individuals. Multiple copies of identical HIV genomes are found in all tissues, indicating that clonal expansions are common in anatomical sites. The majority (>85%) of these expanded clones are shared across multiple tissues. These findings suggest that infected cells expand, migrate, and possibly circulate between anatomical sites. [Display omitted] • In people on ART, half the HIV genomes in tissues are clonally expanded • Genetically intact HIV proviruses are more often found in lymphoid tissues • Identical proviral sequences are frequently found in distant tissues Dufour et al. study viral reservoirs by analyzing multiple samples from two men who donated their bodies for HIV cure research. They show that genetically intact proviruses are more often found in lymphoid organs. Moreover, half of the HIV genomes in tissues are clonally expanded and are frequently located in distant compartments. [ABSTRACT FROM AUTHOR]