Klonopin (clonazepam) has not been studied well enough in pregnant women to be recommended during pregnancy. There have been reports of associated birth defects and withdrawal symptoms in neonates of mothers taking clonazepam and other benzodiazepines.
In addition, there have been animal studies that have shown an increase in birth defects. While there are risks of taking clonazepam during pregnancy, there may also be risks of being left untreated for your condition. Consult your physician to develop your plan during the course of your pregnancy and to better understand the risk versus benefit. It may be necessary to continue therapy depending on the situation.
Using clonazepam or other benzodiazepines immediately prior to during child birth may result in adverse effects for the neonate including respiratory depression and difficulty feeding. Use during later stages of pregnancy has been shown to cause withdrawal symptoms for the neonate after birth.
The FDA has recently changed the required information for drug labeling in regards to pregnancy risks. Between 1979 and 2015, manufacturers were required to use risk categories of either A, B, C, D, or X for classification of their drugs. For example, clonazepam was previously considered a Category D, which meant there has been evidence of at least some risk to the baby.
Most benzodiazepines were classified as Category D and some are even Category X and should never be given during pregnancy like temazepam. The FDA has now decided that these categories were not as meaningful as they should be. Now, the FDA requires drug labeling to include more robust information.
Physicians are advised to encourage pregnant patients taking clonazepam to enroll in the NAAED Pregnancy Registry which can be done online at http://www.aedpregnancyregistry.org/ or via phone at 1-888-233-2334.
Source: Klonopin package insert