We investigated the association between nutrient biomarkers and dietary intake estimated using a brief self-administered dietary history questionnaire (BDHQ) for Japanese children and adolescents. Blood samples were collected from 398 subjects (5th graders of elementary school aged 10-11 y, and 2nd graders of secondary schools aged 13-14 y) randomly selected from among students in Shunan City, Japan, who were then required to answer two questionnaires. Spearman correlations were calculated between dietary intake and the corresponding biomarkers (serum carotenoids, tocopherols, and erythrocyte fatty acids). Correlations with β-carotene and β-cryptoxanthin were significant in the 13- and 14-y age group (r=0.220-0.333, p<0.030) and the 10- and 11-y age subgroup who answered the questionnaire with assistance (r=0.295-0.299, respectively, p=0.006). Consumption of green-yellow vegetables and fruits was significantly correlated with β-carotene and β-cryptoxanthin levels (r=0.205-0.341, p<0.047). In the 13- and 14-y age group, correlations with eicosapentaenoic and docosahexaenoic acids were between 0.215 and 0.473 (p<0.040). Total seafood intake was significantly correlated with marine n-3 polyunsaturated fatty acids (PUFAs; r=0.239-0.420, p<0.023). In the 10- and 11-y age subgroup who completed the questionnaire with assistance, seafood intake was significantly correlated with marine n-3 PUFAs (r=0.239-0.243, p<0.032). In conclusion, dietary intake assessed using the BDHQ reflects the corresponding biomarkers for 13- and 14-y-olds; however, when used for elementary school children, caution is necessary in interpreting the results.