Acute Trypanosoma cruzi infection induces alterations in both lymphoid and microenvironmental compartments of the thymus. This prompted us to investigate whether the lymphoepithelial complex thymic nurse cell (TNC) was comprised in the thymic pathology occurring in experimental Chagas' disease. The isolation of TNCs from acutely T. cruzi-infected mice revealed a reduction in TNC numbers that paralleled thymic atrophy. This decrease does not seem to be stress-related since it was not seen following glucocorticoid hormone injection. Moreover, an increased intra-TNC cell death in complexes from infected animals was noticed. In addition, acute T. cruzi infection induced a decrease in size and granularity of TNC complexes, as well as several ultrastructural alterations indicating cell damage. The epithelial component of TNCs, independent of being infected in vitro or derived from infected animals, showed an enhancement of extracellular matrix proteins that is likely related to the enhanced thymocyte release observed in these complexes. Conjointly, these data show that TNCs are importantly affected in acute experimental T. cruzi infection, possibly contributing to the previously observed alterations in thymocyte differentiation.