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Background: The objective of this study is to investigate the magnitude and nature of health inequalities between indigenous (Scheduled Tribes) and non-indigenous populations, as well as between different indigenous groups, in a rural district of Kerala State, India. Methods: A health survey was carried out in a rural community (N= 1660 men and women, 18-96 years). Age- and sex-standardised prevalence of underweight (BMI<18.5 kg/m2), anaemia, goitre, suspected tuberculosis and hypertension was compared across forward castes, other backward classes and tribal populations. Multi-level weighted logistic regression models were used to estimate the predicted prevalence of morbidity for each age and social group. A Blinder-Oaxaca decomposition was used to further explore the health gap between tribes and non-tribes, and between subgroups of tribes. Results: Social stratification remains a strong determinant of health in the progressive social policy environment of Kerala. The tribal groups are bearing a higher burden of underweight (46.1 vs. 24.3%), anaemia (9.9 vs. 3.5%) and goitre (8.5 vs. 3.6%) compared to non-tribes, but have similar levels of tuberculosis (21.4 vs. 20.4%) and hypertension (23.5 vs. 20.1%). Significant health inequalities also exist within tribal populations; the Paniya have higher levels of underweight (54.8 vs. 40.7%) and anaemia (17.2 vs. 5.7%) than other Scheduled Tribes. The social gradient in health is evident in each age group, with the exception of hypertension. The predicted prevalence of underweight is 31 and 13 percentage points higher for Paniya and other Scheduled Tribe members, respectively, compared to Forward Caste members 18-30 y (27.1%). Higher hypertension is only evident among Paniya adults 18-30 y (10 percentage points higher than Forward Caste adults of the same age group (5.4%)). The decomposition analysis shows that poverty and other determinants of health only explain 51% and 42% of the health gap between tribes and non-tribes for underweight and goitre, respectively. Conclusions: Policies and programmes designed to benefit the Scheduled Tribes need to promote their well-being in general but also target the specific needs of the most vulnerable indigenous groups. There is a need to enhance the capacity of the disadvantaged to equally take advantage of health opportunities. [ABSTRACT FROM AUTHOR]