The analysis of samples recovered from the abdominal area of an articulated tapir (Tapirus polkensis) from the Late Miocene (4.5–7 million BP) Gray Fossil Site (GFS) revealed a rich palyno-fauna comprised of about 94% egg/oocyst-like structures and 6% pollen and other palynomorphs. In addition, a group of 6 hickory nuts (Carya) was recovered from the same area suggesting that the samples represent the abdominal contents. The analysis of a sample from immediately outside the tapir produced a sample with 98% pollen and less than 0.5% egg/oocyst-like structures. The size, shape, and general morphology of egg/oocyst-like structures were analyzed with light and scanning electron microscopy and were compared to a variety of intestinal parasites found in extant ungulates, and the Perissodactyla in particular. We also compared fossil structures to the numbers and kind of intestinal parasites recovered from fecal samples from the Baird's tapir (T. bairdii) in Costa Rica and from samples collected from the lowland tapir (T. terrestris) from Ecuador to assess their similarity to our fossil sample. Based on these data, we discuss what role parasites may have played in the biology of T. polkensis during the Late Miocene-Early Pliocene.