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Background Exposure to arsenic through drinking water has been associated with impaired cognitive function in school-aged children in a few cross-sectional studies; however, there is little information on critical windows of exposure.Methods We conducted a population-based longitudinal study in rural Bangladesh. We assessed the association of arsenic exposure, based on urinary arsenic (U-As; twice during pregnancy and twice in childhood), with the development of about 1700 children at 5 years of age using Wechsler Pre-school and Primary Scale of Intelligence [intelligence quotient (IQ)].Results Median maternal U-As in pregnancy was 80 µg/l (10–90 percentiles: 25–400 µg/l). Children's urine contained 35 (12–155) µg/l and 51 (20–238) µg/l at 1.5 and 5 years, respectively. Using multivariable-adjusted regression analyses, controlling for all potential confounders and loss to follow-up, we found that verbal IQ (VIQ) and full scale IQ (FSIQ) were negatively associated with (log) U-As in girls. The associations were consistent, but somewhat stronger with concurrent arsenic exposure [VIQ: B = −2.4, 95% confidence interval (CI) = −3.8 to −1.1; FSIQ: B = −1.4, 95% CI = −2.7 to −0.1, n = 817), compared with that at 1.5 years (VIQ: B = −0.85, 95% CI = −2.1 to 0.4; FSIQ: B = −0.74, 95% CI = −1.9 to 0.4, n = 902), late gestation (VIQ: B = −1.52, 95% CI = −2.6 to −0.4; FSIQ: B = −1.35, 95% CI = −2.4 to −0.3, n = 874) and early gestation (VIQ: B = −1.23, 95% CI = −2.4 to −0.06; FSIQ: B = −0.92, 95% CI = −2.0 to −0.2, n = 833). In boys, U-As showed consistently low and non-significant associations with all IQ measures. An effect size calculation indicated that 100 µg/l U-As was associated with a decrement of 1–3 points in both VIQ and FSIQ in girls.Conclusion We found adverse effects of arsenic exposure on IQ in girls, but not boys, at 5 years of age.