Confocal endomicroscopy is a novel technique that permits in vivo microscopy of the human gastrointestinal mucosa during ongoing endoscopy, thereby providing optical virtual biopsies. Endomicroscopy has been demonstrated to reveal histological information in a multitude of diseases in the upper and lower gastrointestinal tract in vivo. Most studies have focused on inflammation and neoplasia, such as Barrett's esophagus, gastric cancer, celiac disease, Crohn's disease and ulcerative colitis, or colorectal neoplasias. Endomicroscopy allows obtainment of "smart," targeted biopsies from regions with microscopic alterations rather than having to rely on random untargeted tissue sampling. This reduces the number of biopsies while increasing the diagnostic yield. In addition, immediate histological information is available, enabling immediate therapy. Apart from morphological visualization, endomicroscopy offers a unique possibility to study pathophysiological events in their natural environment (functional imaging). Molecular imaging with endomicroscopy applied in clinical and basic science will permit advances in understanding of the cellular basis of gastrointestinal physiology and pathophysiology.