Oil and gas extraction-related activities produce air and water pollution that contains known and suspected teratogens. To date, health impacts of in utero exposure to these activities is largely unknown. We investigated associations between in utero exposure to oil and gas extraction activity in Texas, one of the highest producers of oil and gas, and congenital anomalies. We created a population-based birth cohort between 1999 and 2009 with full maternal address at delivery and linked to the statewide congenital anomaly surveillance system (n = 2,234,138 births, 86,315 cases). We examined extraction-related exposures using tertiles of inverse distance-squared weighting within 5 km for drilling site count, gas production, oil production, and produced water. In adjusted logistic regression models, we calculated odds of any congenital anomaly and 10 specific organ sites using two comparison groups: 1) 5 km of future drilling sites that are not yet operating (a priori main models), and 2) 5-10 km of an active well. Using the temporal comparison group, we find increased odds of any congenital anomaly in the highest tertile exposure group for site count (OR: 1.25; 95% CI: 1.21, 1.30), oil production (OR: 1.08; 95% CI: 1.04, 1.12), gas production (1.20; 95% CI: 1.17, 1.23), and produced water (OR: 1.17; 95% CI: 1.14, 1.20). However, associations did not follow a consistent exposure-response pattern across tertiles. Associations are highly attenuated, but still increased, with the spatial comparison group in the highest tertile exposure group. Cardiac and circulatory defects are strongly and consistently associated with all exposure metrics. Increased odds of congenital anomalies, particularly cardiac and circulatory defects, were associated with exposures related to oil and gas extraction in this large population-based study. Future research is needed to confirm findings, examine specific exposure pathways, and identify potential avenues to reduce exposures among local populations. About 5% of the U.S. population (~17.6 million people) resides within 1.6 km of an active oil or gas extraction site, yet the influence of this industry on population health is not fully understood. In this analysis, we examined associations between oil and gas extraction-related exposures and congenital anomalies by organ site using birth certificate and congenital anomaly surveillance data in Texas (1999-2009). Increased odds of congenital anomalies, particularly cardiac and circulatory defects, were associated with exposures related to oil and gas extraction in this large population-based study. Future research is needed to confirm these findings.