The possible association between prospectively and medically recorded vulvovaginitis-bacterial vaginosis (VV-BV) and different congenital abnormalities (CA) has not been studied. The data set of the population-based Hungarian Case-Control Surveillance of Congenital Abnormalities between 1980 and 1996 were evaluated, i.e. 22,843 pregnant women who had newborns or fetuses with congenital abnormality (cases) and 38,151 pregnant women who delivered newborn babies without any congenital abnormality (controls). The main outcome measures were different congenital abnormalities. Of 22,843 cases with CA, 1,536 (6.7%) had mothers with VV-BV, while of 38,151 matched controls without CA, 2,698 (7.1%) had mothers with VV-BV in the second and/or third gestational month of pregnancy. Nearly all pregnant women with VV-BV were treated during pregnancy, but a higher risk for the total group of CAs (adjusted POR with 95% CI: 0.95, 0.89–1.02) or any CA group was not found. In addition, the risk for total CAs was significantly lower in cases born to mothers with VV-BV and appropriate treatment than born to mothers with VV-BV but without treatment. Thus maternal VV-BV needs treatment during pregnancy as well, because it helps reduce the rate of preterm birth without a risk for CAs.