Background Patients who have undergone bariatric surgery are at risk for subsequent cholecystectomy. We aimed to identify risk factors for cholecystectomy after laparoscopic Roux-en-Y gastric bypass (LRYGB). Methods We conducted a retrospective case-control study of patients who underwent LRYGB between 2013 and 2015. Cases underwent cholecystectomy because of biliary symptoms after LRYGB. For each case, two controls were selected without subsequent cholecystectomy. Logistic regression analyses were used to identify risk factors. Results Between 2013 and 2015, 1780 primary LRYGBs were performed. We identified 233 (13.1%) cases who had undergone cholecystectomy after a median (IQR) of 12 (8-17) months, and 466 controls. Female gender (OR (95% CI) 1.83 (1.06-3.17)), Caucasian ethnicity (OR (95% CI) 1.82 (1.10-3.02)), higher percent total weight loss (%TWL) at 12 months (OR (95% CI) 1.06 (1.04-1.09)), and preoperative pain syndrome (OR (95% CI) 2.72 (1.43-5.18)) were significantly associated with an increased risk for cholecystectomy. Older age (OR (95% CI) 0.98 (0.96-0.99)) and preoperative statin use were associated with a reduced risk (OR (95% CI) 0.56 (0.31-1.00)). A dose-effect relationship was found between the intensity of preoperative statin and risk for cholecystectomy. Conclusions In our study, higher %TWL and preoperative pain syndrome were associated with an increased risk for cholecystectomy besides the traditional risk factors female gender and Caucasian ethnicity. These factors can be used to identify high-risk patients, who might benefit from preventive measures. Whether statins can protect bariatric patients from developing gallstones should be investigated prospectively.