Bats (order Chiroptera) are known to harbor a large diversity of emerging pathogens, being second only to rodents. Viruses are the most abundant biological entities on the planet, and viruses that have their origin in the animal world cause most of the emerging diseases in humans. Viruses from bats can become important zoonoses, transmitted to domestic animals and humans via bats because of their ability to fly. Until 2012, there was only one report of hantavirus in bats. Then, it was thought that hantaviruses were rodent-insectivore borne pathogens. However new species of hantaviruses have been associated with bats, expanding the potential reservoirs and range of these viruses. To investigate if Neotropical bats harbor hantavirus, we captured 275 bats from February 2012 to April 2014 in south-eastern Brazil. From the captured bats, 53 individuals of different species were tested for hantavirus infection. It was possible to amplify a partial genome of S segment from the frugivore Carollia perspicillata and the common vampire bat Desmodus rotundus. The nucleotide sequences obtained showed high similarity with Araraquara virus, considered to be the most lethal genotype in the Andes virus clade, and perhaps in the world. Yet, we were able to find evidence of hantavirus infection throughout the organs, tissues and urine of D. rotundus. We report here for the first time in the Americas a hantavirus systemic infection in Neotropical bats, and we provide strong evidence that Neotropical bats may be playing a role as reservoirs disseminating lethal hantavirus.