Confocal laser endomicroscopy enables in vivo microscopy of the mucosal layer of the gastrointestinal tract with subcellular resolution during ongoing endoscopy. Endomicroscopy opens the door to immediate tissue and vessel analysis. Different types of diseases can be diagnosed with optical surface and subsurface analysis. Analysis of the in vivo microarchitecture can be used for targeting biopsies to relevant areas, and subsurface imaging can unmask microscopic diseases or bacterial infection. Molecular imaging is becoming feasible, which will enable new indications in gastrointestinal endoscopy. This article reviews the current and rapidly expanding clinical data on endomicroscopy and gives a look into future research.