The widespread use of cross-sectional imaging has led to an increased frequency of incidentally detected pancreatic cysts. Neoplastic cysts such as mucinous lesions and solid pseudo-papillary neoplasms have malignant potential and therefore the early detection of these lesions presents an opportunity for prevention or early detection and management of pancreatic adenocarcinoma. Serous neoplastic lesions and non-neoplastic pancreatic cysts such as pseudocysts or walled off pancreatic necrosis and are not associated with malignant potential. It is important to identify those mucinous lesions with the highest potential of malignancy in order to direct management either towards surveillance or resection. The preoperative diagnosis of these cysts is a challenge as cross-sectional imaging alone is often inadequate at making the diagnosis. Endoscopic ultrasound (EUS) with or without fine-needle aspiration (FNA) can assess the morphology of cysts including identification of high risk characteristics of cysts as well as allowing aspiration of cyst fluid, which can be analyzed for cytology, mucin, tumor markers, amylase and molecular markers. Intraductal papillary mucinous neoplasms (IPMN) have three main subtypes; main duct IPMNs (MD-IPMN), branch duct IPMNs (BD-IPMN) and mixed type IPMNs which have feature of both the aforementioned. MD-IPMNs have the highest malignant potential and are often easier to identify on cross-sectional imaging due to the involvement of the main pancreatic duct. Current guidelines suggest that these lesions should generally be considered for resection without further evaluation. Several guidelines exist for the investigation and management of BD-IPMNs, which have a lower malignant potential and there has been much interest in more clearly defining the role of EUS and EUS-FNA in this group of patients. In this review article we discuss the role of EUS in the diagnosis, risk stratification and management of these lesions.