One important cause of birth defects during pregnancy is cytomegalovirus infection of pregnant women who haven't previously been exposed to the illness. This causes birth defects in about 15 per 100,000 births, despite the fact that children or adults who aren't pregnant when effective suffer only minor symptoms. About a third of women have no previous exposure when they get pregnant.
[R]oughly 27,000 first-time cytomegalovirus infections occur in pregnant women in the United States every year. These women don’t harbor home-grown antibodies — generated from a previous infection — that would lower the risk of re-infection. . . . As a result, such women have a one-in-three chance of passing the virus along to their fetuses via the placenta. At birth, infected babies have an 11 percent chance of having symptoms that include hearing damage, visual impairment, mental retardation and diminished motor skills.
A vaccine now exists for cytomegalovirus, which can cut infections during pregnancy by 50%. But, given the long history of medical treatments aimed at pregnant women that had unintended consequences (DES and thalidomide are among the more notable examples), extreme caution is in order before this is used widely, even though this birth defect pathway in this case appears to be well understood, and vaccination is a well established technique of modern medical science.