Background The majority of literature on the precut technique is concerned with needle-knife sphincterotomy, whereas the comparison of transpancreatic sphincterotomy and needle-knife sphincterotomy has been rarely reported. Aim The aim of the study was to compare the success and the complication rates of transpancreatic sphincterotomy with needle-knife sphincterotomy. Methods During May 2006 and April 2007, 3,178 consecutive endoscopic retrograde cholangiopancreatography (ERCP) procedures were performed in a prospective multicenter study on ERCP-related complications. From the files of these patients, data of cases undergoing precut sphincterotomy, including transpancreatic sphincterotomy and needle-knife sphincterotomy, were retrospectively extracted and analyzed. Results Overall, 216 patients with precut sphincterotomy were identified; 140 cases received transpancreatic sphincterotomy, and 76 received needle-knife sphincterotomy. There was no significant difference in the initial and eventual success rates between transpancreatic and needle-knife sphincterotomy (82.9% vs. 90.8% and 90.0% vs. 90.8%, respectively). The overall incidences of complications and acute pancreatitis were not significantly different between the two groups (14.3% vs. 18.4% and 11.4% vs. 11.8%, respectively). Conclusions Transpancreatic precut sphincterotomy results in similar success and complication rates when compared with needle-knife sphincterotomy. This new precut technique seems to be a safe alternative to needle-knife sphincterotomy with reasonable success rates. However, prospective randomized controlled studies are required to verify our findings.