Fifty-seven Trypanosoma cruzi stocks isolated from Triatoma infestans and Triatoma spinolai of the five different geographic endemic areas of Chile were studied by schizodeme and molecular karyotype analysis. Four different genotypes are found in the sylvatic T. spinolai vector and five in the T. infestans domiciliary vector. Of these genotypes, two common genotypes overlap on both transmission cycles exclusively in the extreme northern endemic areas of Chile. Metacyclic trypomastigotes obtained in vitro or cell-derived trypomastigotes proved to be infective in gamma-irradiated Balb/c mice for the study of the immune response and biological behavior. Of a total of 57 T. cruzi stocks obtained, 19 of them, representing all the different genotypes found in Chile, were tested on a murine experimental model and then fully studied. Female compared with male animals demonstrated greater resistance to Chagas disease with all the T. cruzi stocks tested. The immune response was assessed by lytic antibodies that were studied by the in vitro antibody-dependent complement-mediated lytic assay with the use of bloodstream trypomastigotes as target cells. In one unique parasite genotype the elicited lytic antibodies reacted in a genotype-specific manner, in contrast with lytic antibodies generated by other T. cruzi genotypes. Parasitemias were high, moderate, and low, with mortality ranges of 6-50%, 0-45%, and 0-10%, respectively. No association was found between specific infective genotypes and virulence or mortality. Independently of the T. cruzi strain studied, each population displayed a characteristic parasitemia curve and prepatent period. A considerable number of the parasite stocks proved to be mixed populations, according to molecular karyotype patterns obtained before and after differentiation and amplification of the parasites. This fact created difficulty in assessing the identity of the genotype really infective to mice.