Exposure to methylmercury (MeHg) during the foetal and postnatal periods is known to have adverse effects on children's development. However, little attention has been paid to MeHg exposure during early childhood in Japan. To examine the regional differences in MeHg exposure and seafood consumption and the association between MeHg exposure and seafood consumption and dental metal restorations, we measured the total mercury (T-Hg) concentration in hair as an MeHg exposure index, and using questionnaires, we measured the frequency and amount of seafood consumption and the presence of dental metal restorations in 118 children aged 3-6years in five regions of Japan. The arithmetic and geometric means of the T-Hg concentrations in hair were 1.03 and 0.87ppm, respectively, and approximately 40% of the children exceeded the United States Environmental Protection Agency recommendation of 1.0ppm. Significant regional differences in the hair T-Hg concentrations were found among the five regions, and the regional differences were consistent with the traditional regional patterns of eating fatty fish. According to the regression analysis, the consumption of fatty fish, particularly tuna/swordfish, had a significant effect on hair T-Hg concentrations, whereas age, sex, the materials used for dental metal restorations, and other types of seafood or fish/shellfish had no significant effects.