Here we report the first genome-wide scan performed for caries. Evidence from twin studies suggests a genetic component to caries. We aimed to identify genetic factors contributing to caries in a population similarly influenced by confounding factors, such as diet, oral hygiene habits, fluoride exposure, and access to dental care. Forty-six families with similar cultural and behavioral habits, and living in the Philippines, were studied, and genome-wide genotype data and DMFT (Decayed, Missing due to caries, Filled Teeth) scores were evaluated. Suggestive loci logarithmic odds (LOD) scores above 2.0 or non-parametric p-values below 0.0009) were found for low caries susceptibility (5q13.3, 14q11.2, and Xq27.1) and high caries susceptibility (13q31.1 and 14q24.3). Genes that may be related to saliva flow and diet preferences are proposed as possible candidates. A protective locus for caries in the X chromosome may explain the gender differences seen in caries frequency.