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Background: Human bodies are constantly exposed to heavy metals like mercury due to industrialization and environmental pollution. The health effects of mercury have been a common concern. In particular, children need to be more careful because they are in the stage of growth and development. However, there is no firm consensus about the effects of mercury on neurodevelopment in children. Methods: We describe the association between blood mercury concentrations in 6 years old children (N = 574) and with the Stroop color and word test(SCWT) scores based on the Environment and Development of Children (EDC) study, a prospective cohort study. In the SCWT, the color word score represents the subject's ability to control cognitive interference. Univariate analysis and multivariate analysis consisting of three models were performed with different variables and stratification of gender was also conducted. Results: There was no statistically significant association between the log-transferred prenatal and postnatal blood mercury levels and the ability of interference control in 6 years old children (N = 396). However, when stratified by gender, girl's color-word test score in Model 1 showed a decrement by -3.71 points for each log-transferred blood mercury increment (p-value = 0.0765). This trend persisted in Model2 (Beta: -3.76, p-value = 0.0766) and Model3 (Beta: -4.06, p-value = 0.0547). Conclusions: The result suggests that mercury exposure may affect interference control especially in girls. The color-word score in the SCWT is a score obtained by suppressing the automated reaction to read letters under the condition that the color of word and letter do not match and reflecting the frontal lobe suppression process. The analysis showed that the ability to control cognitive interference may decrease with an increment of log blood mercury concentration.