Background: Benzodiazepine medications can be used to treat anxiety, a condition affecting 15% of women of childbearing age in the United States. Studies have shown conflicting results for the association between benzodiazepine use during pregnancy and birth defects. Methods: We analyzed 1997-2011 data from the National Birth Defects Prevention Study, a multisite, population-based case-control study. We assessed the prevalence of and factors associated with benzodiazepine use in pregnancy among mothers of live-born infants without a birth defect (control mothers). We used logistic regression to estimate adjusted odds ratios (aORs) and 95% confidence intervals (CIs) for the association between specific birth defects and benzodiazepine use; we estimated crude odds ratios (cORs) for defect categories with 3-4 exposed cases.Results: Exposure to benzodiazepines during pregnancy was rare (N = 93/11,614; 0.8%). Benzodiazepine use was more common among control mothers who were ≥30 years, non-Hispanic white, had more education, smoked, and took antidepressant medication. We observed significantly elevated ORs for any benzodiazepine and Dandy-Walker malformation (cOR: 3.1; 95% CI: 1.1, 8.6); for alprazolam and anophthalmia or microphthalmia (cOR: 4.0; 95% CI: 1.2, 13.1) and esophageal atresia or stenosis (aOR: 2.7; 95% CI: 1.2, 5.9); and lorazepam and pulmonary valve stenosis (cOR: 4.1; 95% CI: 1.2, 14.2), but sample sizes were limited and therefore CIs were wide. Conclusions: Our findings suggest that benzodiazepines use is rare and may be associated with risk for certain birth defects. However, these results need replication and should be interpreted with caution.