The authors describe the baseline malaria prevalence and arbovirus seroprevalence among 467 subjects in an ongoing cohort study in rural Amazonia. Most subjects (72.2%) reported one or more previous episodes of malaria, and 15.6% had been hospitalized for malaria, but only 3.6% of individuals five years or older had malaria parasites detected by microscopy (10 with Plasmodium vivax and 4 with P. falciparum). Antibodies to Alphavirus, Orthobunyavirus, and/or Flavivirus were detected by hemagglutination inhibition (HI) in 42.6% of subjects aged five years or older, with a higher seropositivity rate among males (49.2%) than females (36.2%). Since 98.9% of subjects had been immunized for yellow fever, the presence of cross-reactive antibodies to dengue and other Flaviviruses cannot be ruled out, but at least 12 subjects (3.3%) with IgM antibodies to dengue virus detected by ELISA had a putative recent exposure to this virus.