Over 2 yr, we assessed the health of 35 lowland tapirs (Tapirus terrestris) in the Brazilian Cerrado (CE) biome, an area that is highly affected by human activities. This involved physical examinations, hematology and blood biochemistry, urinalysis, fecal parasitologic evaluation, microbial profiling of anatomic cavities and lesions, and serologic surveys for evidence of infectious agents. Research methods closely resembled those used in previous tapir health assessments in the Atlantic Forest (AF) and Pantanal (PA) biomes, allowing for a comparison among the three populations. Although not reaching statistical significance (P>0.05), tapirs from the CE exhibited poorer body and skin condition as compared to animals from the AF and PA. Furthermore, there were higher prevalences of dental problems and traumatic lesions as compared to those from the AF and PA. Eight of the 12 hematologic parameters evaluated and 17 of the 30 biochemical parameters differed significantly (P<0.05) between the tapirs from CE and those from the AF and PA. We isolated 24 different microbiologic strains from swabs of anatomic cavities and dermal lesions, of which five taxa had not previously been found in the AF or PA. We detected serum antibodies to Leptospira interrogans, bluetongue virus, and porcine parvovirus. Overall, our results suggested that tapirs from the CE exhibited more health abnormalities than tapirs in the AF and PA, possibly due to a greater exposure to environmental disturbances in the area.