Left atrial appendage (LAA) exclusion is performed by some surgeons in patients with atrial fibrillation (AF) who undergo coronary artery bypass grafting (CABG). However, the available evidence regarding the efficacy and safety of this procedure remains mixed. We queried the Nationwide Inpatient Survey Database for the 10-year period from 2004 to 2013. Using International Classification of Diseases, Ninth Edition, Clinical Modification diagnosis codes, we identified patients who had a diagnosis of AF and underwent a primary procedure of CABG with or without LAA exclusion. We then performed a 1:5 matching based on the CHA2DS2VASc score between patients who got LAA exclusion and those who did not (control group). The primary outcome was the incidence of in-hospital cerebrovascular events, whereas the secondary outcomes included in-hospital bleeding events, pericardial effusion, cardiac tamponade, postoperative shock, and mortality. Our analysis included a total of 15,114 patients. Patients who underwent LAA exclusion had significantly less incidence of cerebrovascular events (2.0% vs 3.1%, p = 0.002). However, LAA exclusion group had higher incidences of bleeding events (36.4% vs 21.3%, p <0.001), pericardial effusion (2.7% vs 1.2%, p <0.001), cardiac tamponade (0.6% vs 0.2%, p <0.001), and postoperative shock (1.2% vs 0.4%, p <0.001). LAA exclusion was associated with higher in-hospital mortality (1.6% vs 0.3%, p <0.001). Multivariate regression analysis showed that LAA exclusion was significantly associated with lower cerebrovascular accident events and higher in-hospital mortality. In conclusion, LAA exclusion in patients with AF undergoing CABG might be associated with a lower incidence of in-hospital cerebrovascular events. This benefit is offset by a higher incidence of higher bleeding events, pericardial effusion, cardiac tamponade, postoperative shock, and in-hospital mortality.