In the acute phase of Trypanosoma cruzi infection there is a prominent thymus atrophy, which is determined by massive loss of immature CD4/CD8 double positive cells. Recently, the involvement of a parasite transialidase, which is shed from the parasite cell membrane and the activation of P2X(7), a purinergic receptor, were stated as important pathways leading to thymus atrophy. In this work we evaluated the possible involvement of Fas- and perforin-based cytotoxic pathways in the thymus atrophy induced by T. cruzi infection using gld/gld and perforin (-/-) mice. We found similar kinetics of thymus atrophy in mice competent or deficient in both cytotoxic pathways, indicating that both molecules are not directly involved in the thymus atrophy, either inducing cellular death or as co-stimulatory molecules.