Prevalence of Toxoplasma gondii and Neospora caninum antibodies in sera of 325 dogs in 11 villages inhabited by the Tapirapé and Karajá ethnic groups in the south of the Brazilian Amazon was determined by the use of an indirect fluorescence antibody test. Antibodies (cutoff 1:16) to T. gondii were found in 169 (52%) and to N. caninum (cut-off 1:50) in 32 (9.8%) of 325 dogs. Seropositivity for both parasitic infections was widely prevalent in dogs from these villages and was higher in older dogs, indicating post-natal transmission.