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