Human defensins play a fundamental role in the initiation of innate immune responses to some microbial pathogens. Here we show that human defensin alpha-1 displays a trypanocidal role against Trypanosoma cruzi, the causative agent of Chagas' disease. The toxicity of human defensin alpha-1 against T. cruzi is mediated by membrane pore formation and the induction of nuclear and mitochondrial DNA fragmentation, leading to trypanosome destruction. Exposure of trypomastigote and amastigote forms of T. cruzi to defensin alpha-1 significantly reduced parasite viability in a peptide concentration-dependent and saturable manner. The toxicity of defensin alpha-1 against T. cruzi is blocked by anti-defensin alpha-1 immunoglobulin G. Electron microscopic analysis of trypomastigotes exposed to defensin alpha-1 revealed pore formation in the cellular and flagellar membranes, membrane disorganization, and blebbing as well as cytoplasmic vacuolization. Furthermore, human defensin alpha-1 enters the trypanosome when membrane pores are present and is associated with later intracellular damage. Trypanosome membrane depolarization abolished the toxicity of defensin alpha-1 against the parasite. Preincubation of trypomastigotes with defensin alpha-1 followed by exposure to human epithelial cells significantly reduced T. cruzi infection in these cells. Thus, human defensin alpha-1 is an innate immune molecule that causes severe toxicity to T. cruzi and plays an important role in reducing cellular infection. This is the first report showing that human defensin alpha-1 causes membrane pore formation in a human parasite, leading to trypanosome destruction.