Objectives: The subclinical effects of prenatal exposure to methylmercury from fish consumption on the cardiac autonomic function were assessed in 136 Japanese 7-year-old children recruited for this study. Methods: Samples of child’s hair and dry umbilical cord preserved were collected, and hair mercury and cord tissue methylmercury concentrations were determined as current and prenatal exposure biomarkers, respectively. Cardiac autonomic indicators of parasympathetic and sympathetic activities were calculated from the electrocardiographic RR intervals measured. Results: In the children, the cord tissue methylmercury (0.017–0.367, median 0.089 μg/g) was not significantly correlated with the hair mercury (0.43–6.32, median 1.66 μg/g). The cord tissue methylmercury was related negatively to parasympathetic components of cardiac autonomic indicators (P<0.05) and positively to sympathovagal indices (P<0.05), even after correction for possible confounders such as age and sex, although the hair mercury was not significantly correlated with any cardiac autonomic indicators. Conclusions: Despite the potential limitations involved in the retrospective study, these findings suggest that prenatal methylmercury exposure (median of estimated maternal hair mercury at parturition, 2.24 μg/g) may be associated with reduced parasympathetic activity and/or sympathovagal shift.