Introduction: Oral health is essential to well-being and quality of life during childhood. However, among Indigenous children, childhood is characterized by limited coverage of dental services and the lack of continuous preventive programs.

Objective: To analyze the prevalence and severity of dental caries and associated factors among Indigenous children aged three to ten years living in villages served by the Indigenous Health Special District of Bahia (DSEI-BA), Brazil, through a population-based epidemiological survey encompassing the nine health hubs of the DSEI-BA.

Materials and Methods: This cross-sectional epidemiological study was conducted in 2025 among Indigenous peoples receiving healthcare services from the DSEI-BA. Data collection was carried out by dentists, oral health assistants, and undergraduate and graduate students from the School of Dentistry at the Federal University of Bahia. Oral examinations were performed to assess dental caries using the dmft and DMFT indices. In addition, structured interviews were conducted with the children’s caregivers to collect information on sociodemographic and behavioural characteristics, as well as access to healthcare services. Associations were analyzed using Poisson regression with robust variance to estimate adjusted prevalence ratios (PRs) and their respective 95% confidence intervals (95% CIs).

Results: A total of 222 Indigenous schoolchildren aged three to ten years participated in the study. Regarding oral hygiene practices, 91.89% of the children used toothpaste once a day, 91.44% used a toothbrush, and 75.23% did not use dental floss. The prevalence of dental caries was 77.03% in the primary dentition and 27.93% in the permanent dentition. In the multivariable analysis, the presence of dental caries in the primary dentition remained associated with dental pain in the previous 12 months (PR = 1.26; 95% CI: 1.09–1.43). In the permanent dentition, dental caries was associated with being aged 7–10 years (PR = 2.96; 95% CI: 1.84–4.76) and not having attended a dental appointment during the previous year (PR = 1.54; 95% CI: 1.04–2.30).

Conclusion: Dental caries is a highly prevalent oral health condition among Indigenous children in Bahia, Brazil. A broader understanding of the oral health conditions of Indigenous peoples is essential to strengthen preventive initiatives, with particular emphasis on family-centred oral health education.