OBJECTIVE Universal screening for substance use during pregnancy, brief intervention, and referral to treatment (SBIRT) is recommended by ACOG and the USPSTF. Here we present the implementation of SBIRT into the electronic health record (EHR) to inform clinical intervention and collect data on the prevalence of substance use during pregnancy at three prenatal clinics. METHODS A literature-based SBIRT instrument was developed. The tool was integrated into the EHR of a resident Ob/Gyn clinic, an MFM practice, and an Ob/Gyn generalist practice at our institution, an academic, tertiary care medical center in an urban area, and automated reports of aggregate retrospective EHR data were used to monitor patient responses to SBIRT over time. Data reports included patient responses to screening for substance use, brief intervention, and referral to treatment from January to December 2018 RESULTS: An interprofessional team of health care providers and systems analysts guided the SBIRT implementation process. As of December 2018, overall SBIRT performance during prenatal care encounters was 1797/2619 (69%), 432/1350 (32%), and 1290/1518 (85%) in the resident clinic, MFM practice, and generalist practice, respectively. Eighty (5.1%) women in the resident clinic, 2 (0.5%) in the MFM practice and 14 (1%) in the generalist practice reported past or present substance use. CONCLUSIONS Integrating universal SBIRT into prenatal care using the EHR requires a multi-disciplinary approach. The SBIRT tool facilitates reportable substance use screening, brief intervention, and referral to treatment during prenatal care. Future reports will further characterize substance use in our prenatal practices and inform intervention strategies in this population.