Species of the genus Leishmania parasitize mammals and have life cycles that alternate between vertebrate and invertebrate hosts. Most species develop in a hematophagous arthropod and infect a specific vertebrate host that may belong to diverse orders and families. Visceral leishmaniasis is a chronic zoonosis with a wide geographic distribution, affecting 350 million people globally, mostly in areas with a high risk of infection. In Brazil, this disease not only has a high incidence but is also expanding to new areas, both in urban centers and rural areas, including territories with tribal communities, due to increasing human intervention. The objective of this study was to perform cathepsin L-like gene-based molecular diagnosis of Leishmania infantum in the indigenous Tapirapé ethnic group in the state of Mato Grosso. From the 372 individuals assessed, only 0.8% (3/372) tested positive for L. infantum, all from the same village (Urubu Branco). Despite the small number of infected individuals, this study demonstrates the first human cases of Leishmania infantum infection in this population, suggesting the need for regular monitoring of visceral leishmaniasis in the area and leading to a broad discussion on the planning and implementation of public health measures for the indigenous population, while respecting their distinctive territories and culture.