Background and aim Endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) is commonly used to obtain tissue external to the gastrointestinal tract. EUS-FNA is relatively safe, but occasionally adverse events have been reported. There is scarcity of data on risk factors of adverse events. The aim of this study is to identify risk factors associated with EUS-FNA. Methods In this multicenter case-control study, we retrospectively reviewed 4,097 cases between 2009 and 2012 at 15 hospitals in Korea. Among the patients there were 104 cases (2.5%) who had adverse events of which 12 (0.29%) were severe. We matched 520 controls (1:5 ratios) stratified by hospital to analyze the potential risk factors. Results The most common adverse events were pancreatitis (45/104, 43.3%) and infection (46/104, 44.2%). Endoscopic retrograde cholangiopancreatography (ERCP) on the same day was a risk factor of all adverse events [OR = 2.41, 95% CI (1.41, 4.12)], pancreatitis [OR = 2.31, 95% CI (1.02, 5.25)], and infection [OR = 2.75, 95% CI (1.31, 5.78)]. More than 15 to-and-fro movements during puncture increased the risk of pancreatitis [OR = 2.30, 95% CI (1.11, 4.77)] and infection [OR = 3.65, 95% CI (1.55, 8.59)]. A higher number of punctures was positively correlated with pancreatitis [OR = 1.34, 95% CI (1.08, 1.67)] but negatively correlated with infection [OR = 0.66, 95% CI (0.48, 0.89)]. Conclusions EUS-FNA is a safe procedure in which serious adverse events are rare. We define some risk factors of adverse events during EUS-FNA, including ERCP on the same day, a higher number of punctures, and more than 15 to-and-fro movements.