Microbial translocation is a key cause of systemic immune activation in chronic HIV infection. This study shows that circulating microbial products, likely from the gastrointestinal tract, are a primary cause of HIV-related immune activation. Circulating lipopolysaccharide, an indicator of microbial translocation, is significantly increased in chronically HIV-infected individuals and SIV-infected rhesus macaques. Monocytes are chronically stimulated in vivo by increased lipopolysaccharide, which correlates with measures of innate and adaptive immune activation. Effective antiretroviral therapy appears to reduce microbial translocation. In non-pathogenic SIV infection of sooty mangabeys, microbial translocation does not occur. These findings establish a mechanism for chronic immune activation in the context of a compromised gastrointestinal mucosal surface and provide new directions for therapeutic interventions that modify the consequences of acute HIV infection.Microbial translocation is a key cause of systemic immune activation in chronic HIV infection. This study shows that circulating microbial products, likely from the gastrointestinal tract, are a primary cause of HIV-related immune activation. Circulating lipopolysaccharide, an indicator of microbial translocation, is significantly increased in chronically HIV-infected individuals and SIV-infected rhesus macaques. Monocytes are chronically stimulated in vivo by increased lipopolysaccharide, which correlates with measures of innate and adaptive immune activation. Effective antiretroviral therapy appears to reduce microbial translocation. In non-pathogenic SIV infection of sooty mangabeys, microbial translocation does not occur. These findings establish a mechanism for chronic immune activation in the context of a compromised gastrointestinal mucosal surface and provide new directions for therapeutic interventions that modify the consequences of acute HIV infection.