Phenobarbital has been used to treat epilepsy for nearly a hundred years. Despite its long history of use, data on phenobarbital exposure during pregnancy is limited, and more information is needed to better assess the risks to the fetus. The purpose of this study was to provide additional information about first trimester phenobarbital exposure during pregnancy in relation to major structural defects, minor structural defects, and being small for gestational age. The study design was a prospective observational cohort study comparing women exposed to phenobarbital during pregnancy to non-exposed pregnant women. The study was conducted by the California Teratogen Information Service and Clinical Research Program (CTIS), which collected data on 752 live births from 1978 to 2007. In the study 83 pregnancies were phenobarbital monotherapy exposed, 91 were phenobarbital polytherapy exposed, and 578 pregnancies were non-exposed. All pregnancies were prospectively enrolled in the cohort. Of the 752 live births 69.94% received a blinded dysmorphological exam for major and minor structural defects. Analysis of the data included descriptive statistics, bivariate analysis, and forward stepwise logistic regression. After controlling for cigarette use, the odds of having a baby with at least one major structural defect were 3.950 (95% CI: 1.171, 13.323) times greater among women exposed to phenobarbital monotherapy than among the non-exposed; for the phenobarbital polytherapy group, the odds of having a baby with at least one major structural defect were 8.895 (95% CI: 3.430, 23.071) times greater than for the non-exposed. Review of the types of major structural defects that occurred revealed a higher percentage of infants born with microcephaly in the exposed groups when compared to the non-exposed group. When looking at minor structural defects, after controlling for alcohol use during pregnancy for the phenobarbital monotherapy group the odds of having a baby with three or more minor structural defects were 5.354 (95% CI: 2.708, 10.587) times greater than among the non-exposed group. For the phenobarbital polytherapy group the odds of having a baby with three or more minor structural defects were 7.562 (95% CI: 3.950, 14.477) times greater than among the non-exposed group after controlling for alcohol use during pregnancy. From these results we conclude that there is an increased risk of having a baby with a major structural defect after prenatal exposure to phenobarbital monotherapy or polytherapy in the first trimester. The study also suggests there may be an increased risk for having a baby with three or more minor structural defects after exposure to phenobarbital monotherapy or polytherapy in the first trimester. No statistically significant association was found between phenobarbital exposure during the first trimester of pregnancy and having a baby small for gestational age. Further research is needed to evaluate the risks associated with phenobarbital use during pregnancy in order to provide the most accurate information to pregnant women and health professionals about this exposure.