PURPOSE: The ideal treatment for choledocholithiasis should be simple, readily available, reliable, minimally invasive and cost-effective for patients. We performed this study to compare the benefits and drawbacks of different laparoscopic approaches (transcystic and choledochotomy) for removal of common bile duct stones. METHODS: A systematic search was implemented for relevant literature using Cochrane, PubMed, Ovid Medline, EMBASE and Wanfang databases. Both the fixed-effects and random-effects models were used to calculate the odds ratio (OR) or the mean difference (MD) with 95% confidence interval (CI) for this study. RESULTS: The meta-analysis included 18 trials involving 2,782 patients. There were no statistically significant differences between laparoscopic choledochotomy for common bile duct exploration (LCCBDE) (n = 1,222) and laparoscopic transcystic common bile duct exploration (LTCBDE) (n = 1,560) regarding stone clearance (OR 0.73, 95% CI 0.50-1.07; P = 0.11), conversion to other procedures (OR 0.62, 95% CI 0.21-1.79; P = 0.38), total morbidity (OR 1.65, 95% CI 0.92-2.96; P = 0.09), operative time (MD 12.34, 95% CI -0.10-24.78; P = 0.05), and blood loss (MD 1.95, 95% CI -9.56-13.46; P = 0.74). However, the LTCBDE group showed significantly better results for biliary morbidity (OR 4.25, 95% CI 2.30-7.85; P<0.001), hospital stay (MD 2.52, 95% CI 1.29-3.75; P<0.001), and hospital expenses (MD 0.30, 95% CI 0.23-0.37; P<0.001) than the LCCBDE group. CONCLUSIONS: LTCBDE is safer than LCCBDE, and is the ideal treatment for common bile duct stones.