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The chronic stage of HIV-1 infection has been extensively described as a slowly evolving phase, in which the virus induces T-cell death slightly faster than the human body is able to recover. In contrast, T-cell and viral replication dynamics during primary infection have been less well studied. Recent studies in the SIV–macaque model and in HIV-positive patients during the acute infection period have highlighted the massive and irreversible depletion of CD4 memory T cells in the mucosa, particularly in the gut. Hence, gut-associated lymphoid tissue (GALT) plays a central role in the early stages of HIV-1 pathogenesis. Due to its particular cytokine expression pattern, GALT may favour the differential replication of certain HIV-1 subtypes during primary infection, particularly of subtype C. This could enhance the chance of a successful transmission. Moreover, these early events taking place in GALT during primary infection have major implications for therapy and vaccine design.