Background and study aims: Although endoscopic ultrasound (EUS)-guided transmural drainage (EUD) is preferred over conventional transmural drainage (CTD) of pancreatic pseudocysts by endoscopy in many centers, its superiority with respect to technical success and clinical outcome has not yet been demonstrated in a prospective randomized trial. We conducted this prospective randomized trial to compare the technical success and clinical outcomes of EUD and CTD in treating pancreatic pseudocysts. Patients and methods: A total of 60 consecutive patients with pancreatic pseudocysts were randomly divided into two groups to undergo either EUD (n = 31) or CTD (n = 29) of pancreatic pseudocysts. The technical success rate, complications, and short-term and long-term results were prospectively evaluated. Results: The rate of technical success of the drainage was higher for EUD (94 %, 29/31) than for CTD (72 %, 21/29; P = 0.039) in intention-to-treat analysis. In cases where CTD failed (n = 8), because the pseudocysts were nonbulging, a crossover was made to EUD, which was successfully performed in all these patients. Complications occurred in 7 % of the EUD and 10 % of the CTD group (P = 0.67). During short-term follow-up, pseudocyst resolution was achieved in 97 % (28/29) in the EUD group and in 91 % (19/21) in the CTD group (P = 0.565). Long-term results analyzed on a per-protocol basis showed no significant difference in clinical outcomes between EUD (89 %, 33/37) and CTD (86 %, 18/21, P = 0.696). Conclusions: We found that EUD and CTD can both be considered first-line methods of endoscopic transmural drainage of bulging pseudocysts, whereas EUD should be preferred for nonbulging pseudocysts.