Inhabitants of the high-level natural radiation areas (>1 mSv year⁻¹) of Kerala in southwest India were evaluated for basal damage (spontaneous DNA strand breaks and alkali-labile sites) by the alkaline comet assay and oxidative DNA damage (ENDO III- and hOGG1-sensitive sites) by the enzyme-modified comet assay. Of the 67 adult male subjects studied, 45 were from high-level natural radiation areas and 22 subjects were from a nearby normal-level natural radiation area (≤1 mSv year⁻¹). Basal damage due to the age and residential area (normal-level natural radiation area/high-level natural radiation areas) of the donors showed significant interaction (P < 0.001) when all subjects were analyzed using a general linear model (GLM). In subgroup analysis, basal damage increased with age in subjects from the normal-level natural radiation area (P = 0.02), while a significant negative correlation (P = 0.002) was observed in subjects from high-level natural radiation areas. Further, basal damage in elderly subjects from high-level natural radiation areas was significantly (P < 0.001) lower compared to the subjects from the normal-level natural radiation area. Oxidative DNA damage was not influenced by age, smoking habit or residential area in the entire sample. However, in a subgroup analysis, hOGG1-sensitive sites showed a significant increase with age in subjects from high-level natural radiation areas (P = 0.005). ENDO III-sensitive sites increased with natural radiation exposure in subjects from high-level natural radiation areas (P = 0.02), but when stratified according to smoking, a significant increase was observed only in smokers (P = 0.01). To the best of our knowledge, this is the first study on basal and oxidative DNA damage in healthy adults of this population. However, our findings need more validation in a larger study population.