The goals of this study were to evaluate the effect of the Canova medication, a homeopathic immune-system modulator, on the evolution of infection induced by the Trypanosoma cruzi Y strain in mice. The animals were divided into five groups: (i) untreated infected controls (I), (ii) infected animals treated with benznidazole (Bz), (iii) infected animals treated with the Canova medication (CM), (iv) infected animals treated with benznidazole and the Canova medication (Bz+CM), and (v) uninfected controls that received only the vehicle (grain alcohol) (C). The parameters evaluated were: parasitemia, mortality, control of cure, and tissue parasitism analysis. Our results showed that the evolution of the experimental infection was modified by treatment with CM, and that daily and consecutive doses were harmful to the animals, causing death in 100% of the infected animals in a brief period. The analysis of parasitism performed on the organs on the 12th day postinfection showed that in infected animals treated with CM, the number of amastigote/nests in the spleen was significantly reduced, while in cardiac tissue, intestine, and liver the number was significantly increased compared with infected control animals. These results indicate that CM has a negative influence on the host-parasite relationship, modifying the tropism of the parasite for tissues, and increasing the parasitemia peak in this experimental model.