Pancreatic cysts are mostly incidental findings on computed tomography or magnetic resonance imaging scans, with few patients presenting with abdominal pain or other symptoms. The accurate diagnosis of cysts is important as management depends on the type (neoplastic or non-neoplastic). Cross-sectional imaging is fast being replaced with endoscopic ultrasound (EUS) and various techniques based on that such as EUS-guided fine needle aspiration, EUS-guided needle confocal laser endomicroscopy, EUS-through-the-needle biopsy, and contrast-enhanced EUS. Clinical studies have reported varying diagnostic and adverse event rates with these modalities. In addition, American, European, and Kyoto guidelines for the diagnosis and management of pancreatic cysts have provided different recommendations. In this editorial, we elaborate on the clinical guidelines, recent studies, and comparison of different endoscopic methods for the diagnosis of pancreatic cysts.