Background. Magnetic resonance imaging (MRI) and endoscopic ultrasound (EUS) are considered useful techniques in the evaluation of pancreatic cysts. Aim of this study was to prospectively compare the diagnostic value of these techniques. Methods. This study included consecutive patients who underwent MRI, EUS, and EUS-FNA for a pancreatic cyst that was eventually resected surgically. Observers scored for cyst characteristics, a distinction between mucinous and non-mucinous cysts and a suspicion of malignancy. The interobserver agreement between MRI and EUS was calculated. Results. A total of 32 patients were included. Sensitivity for diagnosing a mucinous cyst was 78% for EUS versus 91% for MRI. Sensitivity for detecting malignancy was 25% (1/4) and 50% (2/4) for EUS and MRI respectively. Sensitivity of EUS-FNA for diagnosing a mucinous cyst (positive cytology and/or CEA >192 ng/ml) was 61%. Sensitivity for detecting malignancy (positive cytology) was 1/4 (25%). Interobserver agreement between MRI and EUS for the features was poor to fair. Conclusion. MRI and EUS are comparable techniques for the morphological characterization of pancreatic cysts. Combined sensitivity of EUS and MRI was higher than the sensitivity of one of the techniques alone. For diagnosing a mucinous cyst, FNA findings showed a low sensitivity, but a high specificity.