Nanotoxicity by quantum dots (QDs) has been extensively studied in prokarionte and eukaryonte cells. In this context, we are using QDs capped with mercaptoacetic acid synthetized in an aqueous medium in order to evaluate the nanocytotoxicity effects as cell death by autophagy in Trypanosoma cruzi. To check this fact, we used two kinds of autophagy markers: 3 methyladenine autophagy (3-MA) a phosphatidylinositol 3- kinase (PI3k) inhibitor and monodansylcadaverine (MDC) a lisossomotropic fluorescent compound useful for identifying cadaverine protein present in the autophagic vacuoles. The quantification of control parasites, 3-MA treated parasites and/or incubated with two QDs concentrations (2 and 200 μM) was made from the growth curves. Then, the same samples were processed for transmission electron microscopy (TEM) and labeling of autophagic vacuoles by MDC was qualitatively analyzed. The results from the growth curve indicated a decrease in parasite numbers incubated with 200μM QDs when compared to parasites incubated with 2μM QDs and the control group. In contrast, parasites incubated with 200μM QDs and treated with 10 and 15mM of 3-MA showed a dose-dependent reversion of cell death by 10% and 15% respectively. The parasite treated by MDC demonstrated many autophagic vacuoles. Also, we found ultrastructural morphological changes in parasites incubated with 2μM and 200μM QDs when compared to control group. Our results show that high QDs concentrations are toxic to T. cruzi, inducing cell death by autophagy.