In 2008, in the west zone of Rio de Janeiro municipality—Brazil, the leishmaniasis control program identified 155 dogs with titers ≥40 by Indirect ImmunoFluorescence (IIF) on blood collected onto filter paper. The objective of this study was to describe the laboratory test findings performed in dogs euthanized by the leishmaniasis program control of Rio de Janeiro municipality. Dogs were examined, subjected to euthanasia and collection of clinical specimens. Parasite isolation was obtained in 29 animals: Leishmania chagasi was isolated in 14 dogs; Leishmania braziliensis was isolated in five dogs; Trypanosoma caninum was obtained in seven animals and one dog had mixed infection (L. braziliensis and L. chagasi). By Polymerase Chain Reaction, seventeen animals were positive in intact skin fragments. In the serological reassessment of serum samples, 28% and 22% were positive for IIF and enzyme immunoassay, respectively. Ninety-one (59%) dogs were negative for all tests performed in this study. The findings indicate that the visceral leishmaniasis control program needs to be adjusted in order to avoid non-infected dogs from being removed or permit that dogs infected with L. chagasi to remain undetected in endemic areas.