Fossil evidence suggests that scent glands are basal features of Testudines. However, we know little about the structure of these glands in the Brazilian Kinosternidae. In this study, we described the macroscopic anatomy, histology, and histochemistry of the scent glands of three males and three females of Kinosternon scorpioides scorpioides from the Marajó mesoregion, Pará State, Brazil. In all of the specimens analyzed, regardless of sex, we found four scent glands, including two axillary and two inguinal glands that were structurally similar to each other. Each gland consisted of a single holocrine secretory lobule, a large lumen surrounded by relatively thin glandular secretory epithelium, an adjacent narrow layer of loose connective tissue, and a thick layer of skeletal striated muscle tissue surrounded by a serous tunic. The secretory epithelium produced a characteristic malodorous yellowish substance that was passed via a single duct through a bone channel in the bridge connecting the carapace to the plastron, and excreted through an outer pore in the plate of each respective gland. Histologically, the secretory epithelium presented cells with two types of secretory vacuoles. Type 1 vacuoles stained red, were the largest and most frequently found, and stained positively with Periodic acid-Schiff (PAS), suggesting they contained glycoproteic complexes. Type 2 vacuoles were translucent, smaller in size and fewer in number, and negative for PAS staining. Because they are very primitive structures, scent glands must play important roles in the lives of chelonians, but their real function remains unknown. Several hypotheses suggest that they can act as protection against ectoparasites, as a repellent of predators, in addition to attracting mates and eliciting other pheromonal responses. In this study, all animals reacted by exuding malodorous substances when handled, as a form of defense. However, these are just assumptions that need to be clarified with additional studies on animal behavior. This article is protected by copyright. All rights reserved.