Background Biliopancreatic diversion with duodenal switch (BPD/DS) is a procedure that has long been considered to have a higher early postoperative morbidity than Roux-En-Y gastric bypass (RYGB). However, patients who undergo BPD/DS have more baseline co-morbidities that may affect the reported early postoperative morbidity. Objective To compare 30-day postoperative morbidity and mortality between BPD/DS and RYGB propensity score-matched cohorts obtained from the MBSAQIP database. Setting Analysis of data obtained from the Metabolic and Bariatric Surgery Accreditation and Quality Improvement Program (MBSAQIP) database. Methods Retrospective analysis of 21-variable propensity score-matched patients in the BPD/DS and RYGB groups obtained from the MBSAQIP database between 2015 and 2019. Variables included age, sex, body mass index, American Society of Anesthesiologists (ASA) class, and pertinent medical co-morbidities. Data were analyzed for 30-day postoperative morbidity, mortality, reoperation, reintervention, and readmissions. Results Before matching, RYGB and BPD/DS cohorts contained 134 188 and 5079 patients, respectively. After multivariable propensity score matching, each cohort contained 5050 patients. The RYGB group had a higher rate of surgical-site infections than the BPD/DS group (1% versus .5%, P = .007) and a higher rate of blood product transfusions (1.1% versus .6%, P = .018). The rate of other early postoperative complications was similar between the 2 groups (P > .05). There was no statistically significant difference in the 30-day mortality, readmission rate, reoperation rate, or reintervention rate between the 2 groups (P > .05). Conclusion When matched for baseline body mass index and co-morbidities, BPD/DS does not lead to a higher 30-day postoperative morbidity and mortality than RYGB. Patients can be counseled that in the short term, BPD/DS is as safe as RYGB.