To compare and assess oral health status of 5-year-old Aborigine children with similar aged, marginalised children in coastal region of south western India. Materials and methods: A total of 418 Aborigine children were invited to participate in the study and a total of 428, 5-year-olds were selected randomly for comparison from other government schools to form the other marginalised group. The WHO (1997) proforma was used for clinical examinations. Chi Square test was used to compare between categorical variables. Mann–Whitney U-test was used for comparison between the two groups for quantitative variables. Logistic and linear regression analysis was performed to determine the importance of the factors associated with caries status. Odds ratio was calculated for all variables with 95% confidence intervals. P £ 0.05 was considered as statistically significant. Results: Dental fluorosis was present in 50 (11.9%) Aborigine children, whereas in the other marginalised group 7 (1.6%) children had dental fluorosis (P £ 0.001). Untreated dental caries was 76.3% for the Aborigine children and 70.3% in the comparison group. Mean dmft values in the two groups were 4.13 ± 3.90 and 3.58 ± 3.60, respectively (P > 0.01). High frequency of between-meal sugar consumption was related to dental caries (OR = 1.20; P = 0.001). Utilisation of dental care and dental fluorosis were inversely related to dental caries (OR = 1.16; P = 0.001 and OR = 1.91; P = 0.001). Conclusion: The study revealed poor oral health status among both the marginalised groups. Significant differences were noted between the two groups with respect to oral hygiene practices, dietary habits, and dental utilisation pattern. Schools for tribal children, male gender, low frequency of cleaning teeth and higher in between meal sugar consumption were significantly related to dental caries.