In the modern era of high-quality cross-sectional imaging, pancreatic cysts (PCs) are a common finding. The prevalence of incidental PCs detected on cross-sectional abdominal imaging (such as CT scan) is 3%-14% which increases with age, up to 8% in those 70 years or older. Although PCs can be precursors of future pancreatic adenocarcinoma, imaging modalities such as CT scan, MRI, or endoscopic ultrasound with fine-needle aspiration (EUS-FNA) are suboptimal at risk stratifying the malignant potential of individual cysts. An inaccurate diagnosis could potentially overlook premalignant lesions, which can lead to missed lesions, lead to unnecessary surveillance, or cause significant long-term surgical morbidity from unwarranted removal of benign lesions. Although current guidelines recommend an EUS or MRI for surveillance, they lack the sensitivity to risk stratify and guide management decisions. Needle-based confocal laser endomicroscopy (nCLE) with EUS-FNA can be a superior diagnostic modality for PCs with sensitivity and accuracy exceeding 90%. Despite this, a significant challenge to the widespread use of nCLE is the lack of adequate exposure and training among gastroenterologists for the real-time interpretation of images. Better understanding, training, and familiarization with this novel technique and the imaging characteristics can overcome the limitations of nCLE use, improving clinical care of patients with PCs. Here, we aim to review the types of CLE in luminal and nonluminal gastrointestinal disorders with particular attention to the evaluation of PCs. Furthermore, we discuss the adverse events and safety of CLE.