The agouti (Dasyprocta leporina) is a New World wild rodent hunted for its meat in Trinidad and other Latin American countries. Studies on agouti under captive conditions have yielded some data on health-related aspects, but relatively very little is known about their wild counterparts. The environment of the agouti can influence the microflora and parasites harbored by the animals, which may contain zoonotic pathogens. Here, the microflora found on the nasal mucosa and sections of the intestinal tract and endoparasites of freshly shot agouti from various areas of Trinidad are described. Staphylococcus epidermidis, S. intermedius, Bacillus spp., Enterobacter spp. and Escherichia coli comprised the majority of bacteria isolated from the nasal mucosa whereas Escherichia coli, Streptococcus viridans, Bacillus spp. and Klebsiella pneumoniae were predominant in all sections of the intestinal tract. The fungi Aspergillus fumigatus, Aspergillus spp., Candida spp., Penicillium spp., and Mucor spp. were only isolated from the nasal cavity but not in any section of the intestinal tract. The parasites Strongyloides spp., Ascaridia spp., a hookworm, a trematode, and Trichuris spp. were detected at variable frequencies in each of the sections of the intestines (small intestine, large intestine, caecum), whereas Eimeria spp. were found in all sections (76.9%, 10 of 13 agoutis). These wild agoutis were presumably healthy at the time of death and represent animals that hunters may encounter. Some of the detected pathogens and parasites have the potential to cause opportunistic infections or infestations, especially in immune-compromised hosts.