The Gran Chaco, Bolivia, has a total of seven species of armadillos with the three-banded (Tolypeutes matacus) and nine-banded (Dasypus novemcinctus) the most commonly hunted by the local Isoseño-Guaraní people. Armadillos are known carriers of zoonotic pathogens, including Mycobacterium leprae, Toxoplasma gondii, and Trypanosoma cruzi; thus human handling and consumption of these species may have a significant public health impact. A health assessment that included physical examinations, hematology, plasma biochemical analyses, levels of exposure to selected infectious agents, and endoparasite and ectoparasite identification was performed on nine-banded and three-banded armadillos in the Gran Chaco, Bolivia. Based on clinical findings, the general health of these armadillos was rated as good. However, many of the nine-banded armadillos (64%) had abrasions and wounds, probably related to the capture method. The blood value results from a subset of these armadillos are presented as baseline values for free-ranging populations of both these species in Bolivia. Serologic antibody tests for M. leprae were negative in three-banded (n  =  8) and nine-banded (n  =  2) armadillos. Three-banded armadillos were antibody positive for Eastern equine encephalitis virus (8/8; 100%) and Saint Louis encephalitis virus (5/8; 62.5%). Two of 12 (16.7%) three-banded armadillos tested were antigen positive for Dirofilaria immitis. Nine-banded armadillos were antibody positive for T. gondii (3/9; 33.3%), Eastern equine encephalitis virus (5/8; 62.5%), and T. cruzi (2/9; 22.2%). Two of eight (25%) nine-banded armadillos were antigen positive for D. immitis. A number of endo- and ectoparasites were identified in/on both species of armadillos. Results from this study support the possibility that the handling and consumption of these species by the local Isoseño-Guaraní people may have a public health impact.