Abstract: The prevalence of stunting in Indonesian children under five years of age is approximately 20%. Chronic maternal malnutrition contributes to the risk of stunting by affecting global DNA methylation. In the present study, we aimed to evaluate the levels of 5-methyl-cytosine (5mC) as a surrogate marker of global DNA methylation in buccal swabs and its potential association with the risk of stunting and cognitive performance. The levels of 5mC were measured using an enzyme-linked immunosorbent assay. The Wechsler Preschool and Primary Scale of Intelligence (WPPSI) was used to measure cognitive function. Buccal swab DNA samples and anthropometric data were collected from a total of 231 children aged zero to five years. In this cross-sectional cohort, the prevalence of stunting was 37% in 138 children aged zero to two years and 30% in 93 children aged over two years. The univariable analysis revealed that the levels of 5mC in buccal swab DNA were significantly lower in severely stunted children (median, 2.84; interquartile range IQR, 2.39–4.62) and children aged less than two years (median, 2.81; IQR, 2.53–4.62) than those in normal children (median, 3.75; IQR, 2.80–4.74; P-value, 0.028) and children aged over four years (median, 4.01; IQR, 3.39–4.87; P-value < 0.001), respectively. We also found that the average cognitive scores tended to be low in boys and stunted children, although the differences were not statistically significant. Furthermore, the levels of 5mC found in buccal swab and mouthwash DNA were not associated with cognitive scores.