BACKGROUND Chronic immune activation is a hallmark of HIV infection and has been postulated as major factor in the pathogenesis of AIDS. Recent evidence suggests that activation of immune cells is triggered by microbial translocation through the impaired gastrointestinal barrier. METHODS To determine the association between microbial translocation and disease progression, we have retrospectively analyzed microbial products, viral load and markers of immune activation in a cohort of 37 simian immunodeficiency virus-infected rhesus monkeys, divided in two groups with distinct disease courses. RESULTS As seen in HIV-infected patients, we found elevated levels of lipopolysaccharide (LPS) in infected animals. However, LPS levels or LPS control mechanisms like endotoxin core antibodies or LPS-binding protein did not differ between groups with different disease progression. In contrast, neopterin, a metabolic product of activated macrophages, was higher in fast progressors than in slow progressors. CONCLUSIONS Our data indicate that translocation of microbial products is not the major driving force of immune activation in HIV infection.