Our analysis covers 122 scientific publications about health issues in free-ranging Neotropical ungulates produced between 1990 and 2022, with an emphasis on the epidemiology of infectious diseases and parasites. Most studies focus on parasitology (43.4%) and bacteriology (15.6%), while body condition (0.8%), toxicology (1.6%), virology (6.6%), and health assessments (6.6%) are less studied. Brocket deer (Mazama americana and M. gouazoubira), followed by peccaries (Pecari tajacu and Tayassu pecari), and the lowland tapir (Tapirus terrestris) were the most frequent species surveyed (61.4% of all publications). We detected considerably higher numbers of studies and health topics covered in Brazil (n = 64; 52.5% of the total) compared to other Latin American countries. We emphasize the need for further research focused on poorly known health aspects of Neotropical ungulates that have received little attention in the past, especially the Chacoan peccary (Catagonus wagneri), taruca deer (Hippocamelus antisensis), Northern pudu (Pudu mephistopheles), and the least known Mazama species. Ecotoxicology and pathology studies are necessary to evaluate the impact of agrochemicals and other human disturbances on Neotropical ungulate populations in the wild. We encourage further research on the human impacts and trends of change in the epidemiology of infectious diseases, parasites, and health status of Neotropical wild ungulate populations.