Confocal laser endomicroscopy enables in vivo microscopy of the mucosal layer of the GI-tract with subcellular resolution during ongoing endoscopy. Endomicroscopy opens a new door for 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. Furthermore, subsurface imaging can unmask microscopic diseases - (microscopic colitis) or bacterial infection (Helicobacter pylori), for example. Molecular imaging is becoming feasible, and this will shortly open the door to new indications in gastrointestinal endoscopy. This chapter reviews the currently rapidly expanding clinical data about endomicroscopy and gives a look into future research.