Trypanosoma caninum constitutes the most recent trypanosomatid species infecting dogs in Brazil. Due to the limited data available about this parasite, this study aims to disclose clinical and laboratory findings from 14 dogs naturally infected. The dogs were diagnosed during a cross-sectional survey in Cuiabá (Mato Grosso, Brazil) and followed up at an interval of 3, 6, and 12 mo in order to evaluate the clinical evolution and to investigate the parasite, the DNA, or both in different biological samples (intact skin, cutaneous scar, blood, bone marrow, and lymph node aspirate) by parasitological (culture and smear exam) and molecular (DNA-based tests) methods. Specific anti-T. caninum and anti-Leishmania antibody production was also evaluated. Ten of 14 dogs infected by T. caninum showed a good general state at the time of diagnosis, and this status did not vary during the follow-up. Anti-T. caninum and anti-Leishmania IgG antibodies were detected by IFAT in 10 and 2 animals, respectively. Concomitant infection by Leishmania chagasi was confirmed in 2 dogs, indicating an overlap of endemic areas in Cuiabá. Trypanosoma caninum (parasite or DNA) was found only in the intact skin in all animals examined. Our results suggest that T. caninum infection can be manifested as an asymptomatic case with low humoral immune response.