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We assessed maternal body weight and several prenatal exposures of the parents to tobacco, pregestational diabetes, chronic cardiovascular and respiratory diseases, periconceptional folic acid and multivitamin intake.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Data from the German Network for Congenital Uro\u2010REctal malformations (CURE\u2010Net) were compared with data from the Malformation Monitoring Centre Saxony\u2010Anhalt of the Otto\u2010von\u2010Guericke University in Magdeburg, Germany. Controls were matched to cases by gender and birth year of the child. Crude and adjusted odds ratios (95% confidence intervals) were calculated for potential risk factors using multivariable logistic regression.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In total, 158 ARM patients and 474 healthy infants born between 1993 and 2008 in Germany were included. Maternal age at birth of ARM cases and birth plurality were significantly higher and gestational age and weight significantly lower compared with controls (<jats:italic>p<\/jats:italic>&lt; 0.0001). We observed significantly increased risks for ARMs associated with maternal smoking before conception and the first trimester of pregnancy (odds ratio = 2.23, 95% confidence interval 1.04\u20134.79,<jats:italic>p<\/jats:italic>= 0.039) and maternal chronic respiratory diseases (odds ratio = 29.25, 95% confidence interval 8.22\u2013104.14,<jats:italic>p<\/jats:italic>&lt; 0.0001). No statistically significant increased risk or protective effect was found for the other investigated factors.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>This study suggests an association between the occurrence of ARMs in the offspring and periconceptional maternal smoking as well as maternal chronic respiratory diseases. In addition, there might be a sign of an association for maternal diabetes, although not statistically significant. It can be assumed that the power is far too low to provide reliable estimates. 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