The lowland tapir is one of four species belonging to the Tapiridae family of the Ceratomorpha suborder, similar to Rhinocerotidae. This study describes anatomy with morphometry, histology (hematoxylin and eosin, Masson-Goldner trichrome, Movat pentachrome, mucicarmine, picro-Mallory trichrome) and histochemistry (PAS, AB pH 1.0, AB pH 2.5; AB pH2.5/PAS and HDI) of the upper and lower eyelids, and superficial gland of the third eyelid with the third eyelid, deep gland of the third eyelid, and lacrimal gland. The aim of the work is to show the features of the above-mentioned structures typical only for Tapiridae, as well as to show the presence of similarities and differences between the families forming the order Perissodactyla. The eyelashes on the upper eyelid were long, while those of the lower eyelid were short and much less prominent. In the upper and lower eyelid sebaceous glands, a characteristic simple alveolar gland producing a mucus-like secretion and poorly developed tarsal glands were observed. The marginal zone of the posterior surface of the eyelids was covered by stratified columnar epithelium with 18–21 layers of nucleated cells, while the bulbar zone of these surfaces was covered by cubic multilayer epithelium with 6–11 non-keratinized layers of cells and with sparse goblet cells. In only lower eyelids, numerous lymphoid nodules, diffuse lymphocytes and high endothelial venules were observed. The superficial gland was an acinar complex which secreted mucous and contained plasma cells within the interlobular and interlobular connective tissue. The upper and lower branches of the third eyelid were the shape of a bent “caudal fin” and were composed of hyaline cartilage, and they contained conjunctiva associated lymphoid tissue (CALT). The deep gland was also an acinar complex producing a serous character and having numerous diffuse lymphocytes. The lacrimal gland was an acinar complex producing seromucous secretions and had numerous plasma cells located in the glandular interstitium. The results of our research indicate that the features of the anatomy of the eyelids and orbital region in the lowland tapir are also typical of the family Tapiridae, but also have features common to the families Equidae and Rhinocerotidae. We confirm the presence of poorly developed tarsal glands in both eyelids as well as presence of a palpebral part of the lacrimal gland in the upper eyelid, which is typical only to Tapirus terrestris.