The clinical outcome of Chagas disease is highly variable, mainly because of the heterogeneity ofTrypanosoma cruzi,a parasite for which 2 major phylogenetic groups (I and II) were recently defined. Epidemiological and immunological data indicate that the prevalence ofT. cruziII in patients living in the southern cone of South America correlates with the alterations caused by Chagas disease. We report here that infection withT. cruziII isolates induces 100% mortality in mice, in contrast to infection withT. cruziI isolates, in which almost all mice enter the chronic phase even when a 1000-fold higher inoculum is administered. Trypomastigotes fromT. cruziII strains express and shed significantly higher amounts of frans-sialidase than do those from the T.cruziI lineage. Disorganization of the thymus histoarchitecture associated with the circulating enzyme was observed after infection withT. cruziII strains, in contrast to transient thymus lesions found in mice infected withT. cruziI strains. Therefore, frans-sialidase becomes the first T.cruzivirulence factor identified that is differentially expressed by the main parasite groups and that contributes to their contrasting behaviors.