Chagas disease is caused by Trypanosoma cruzi and dogs are an important reservoir of the parasite as well as a good model for the study of the pathogenesis of the disease. We aimed here at characterizing the immunopathology of naturally infected dogs in Merida, Yucatan, Mexico. Following an initial screening for T. cruzi seropositive stray dogs, we examined 9 seropositive and 10 seronegative animals. High lymphocytes and low monocytes counts were observed in peripheral blood from seropositives dogs. Three of nine seropositive dogs presented electrocardiographic alterations including right bundle branch block, sinusal block and QRS complex alterations and some right ventricle enlargement was noted. Histopathologic analysis of cardiac walls revealed significant inflammation with a clear tropism for the right ventricle, although most walls were affected. Seropositive dogs presented low IgG1 and high IgG2 levels. Higher IgG1 levels were associated with increased cardiac index and myocarditis, suggesting that a Th2 immune response leads to susceptibility and increased disease severity. These observations shed some light on the mechanisms of pathogenesis of Chagas disease in dogs, and provide a good framework for the evaluation of novel drugs and vaccines in this animal model.