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We investigated the relationship between maternal smoking history and congenital anomalies in children. Drawing on data from the Japan Environment and Children's Study collected between January 2011 and March 2014, the smoking habits of pregnant women were categorized as "never smoked," "quit before pregnancy, "quit after pregnancy," and "full smoking." Of the 91 626 participants examined, a total of 2199 (2.4%) infants were born with any congenital anomalies. Logistic regression analysis was used to determine the odds ratio for congenita