Background Although endoscopic ultrasonography (EUS) is a useful tool for diagnosing pancreatobiliary diseases, not many facilities perform this technique as it is difficult to master. Currently, two new EUS systems exist: EU-ME2/GF-UCT260, manufactured by Olympus, and SU-1/EG-580UT, manufactured by Fujifi lm. Some reports have compared new EUS models to older versions, but the operability and image quality of these two latest systems have not been compared. Our study aimed to compare the usefulness of these two types of EUS. Methods Forty consecutive patients were recruited and randomized in a two-arm clinical trial; Arm 1: EU-ME2/GF-UCT260 was used only for observation and SU-1/EG-580UT for EUS-fi ne needle aspiration (FNA); Arm 2: SU-1/EG-580UT was used only for observation and EU-ME2/GF-UCT260 for EUS-FNA. Using a crossover design, we evaluated image fi ndings, ease of scope insertion, and visibility of the gastrointestinal (GI) tract. Each procedure was scored using a 5-point scale (Clinical Trial ID: UMIN000031373). Results SU-1/EG-580UT was signifi cantly better in terms of lesion-delineating capacity: lesion border (P < 0.001), internal echo (P < 0.001). Signifi cantly easier scope insertion was observed with SU-1/EG-580UT with respect to any insertion into the piriform recess (P = 0.018), the pylorus ring (P < 0.001), and the superior duodenal angle (P < 0.001). Visibility during gastrointestinal observation was also significantly better with the SU-1/EG-580UT (P < 0.001) than with the EU-ME2/ GF-UCT260. Conclusion SU-1/EG-580UT EUS demonstrated superior performance during ultrasonic endoscopic GI observation, operability, and ultrasonic image quality. The result of the superior ultrasound imaging quality of SU-1/EG-580UT EUS will aid in the identification of small pancreatic malignancies with unclear borders and prove useful in evaluating mural nodules of IPMN in detail. These findings could result in an increased use of EUS and improve identifi cation and prognosis of patients with pancreatobiliary diseases.