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The objective of the study was to estimate association between maternal glomerulonephritis during pregnancy and structural birth defects, i.e. congenital abnormalities. The prevalence of maternal glomerulonephritis during the first trimester of pregnancy in cases with different congenital abnormalities was compared to that of matched controls without congenital abnormalities in the population-based Hungarian Case-Control Surveillance System of Congenital Abnormalities. Of 22,843 cases with congenital abnormalities, 309 (1.35%) had mothers with glomerulonephritis during pregnancy, compared to 479 (1.26%) of 38,151 controls (adjusted POR with 95% CI = 1.0, 0.9-1.2). Specified groups of congenital abnormalities were also assessed versus controls. Cases with isolated intestinal atresia/stenosis (adjusted POR with 95% CI: 6.8, 1.3-37.4) based on five cases were more likely to have mothers with prospectively and medically recorded glomerulonephritis. In conclusion a higher rate of congenital isolated intestinal atresia/stenosis may be associated with the maternal glomerulonephritis. However, this finding is considered only as signal and further studies are needed to confirm or reject this possible association.