The history of Homo sapiens dispersal around the world and inherent interpopulation contacts and conflicts has given rise to several transitions in his relationships with the natural world, with the final result of changes in the patterns of infectious disease (McMichael  Ecosystem Health 7:107–115). Of particular interest, in this context, is the contact between Amerindians and Europeans that started at the end of the 15th century, and the resulting exchange of microbes. We successfully recovered ancient DNA from a pre-Columbian mummy from Cuzco (Peru), radiocarbon-dated to 980–1170 AD, for which consistent mtDNA amplifications and sequences were obtained. The analysis of mtDNA revealed that the mummy's haplogroup was characteristic of Native American populations. We also investigated a sample of feces directly isolated from the intestines of the mummy, using a polymerase chain reaction system designed to detect the broadest spectrum of bacterial DNAs. The analysis of results, following a criterion of “paleoecological consistency” (Rollo and Marota  Philos. Trans. R. Soc. Lond. [Biol.] 354: 111–119), demonstrated that some vestiges of the original microbial flora of the feces were preserved. In particular, we were able to identify the DNA of Haemophylus parainfluenzae, thus suggesting that this recently recognized pathogen was present in precontact Native Americans. Am J Phys Anthropol, 2006. © 2005 Wiley-Liss, Inc.