Endomicroscopy becomes possible due to the integration of a miniaturized confocal microscope in the distal tip of a conventional endoscope. Endomicroscopy enables subsurface analysis of the gut mucosa and in vivo histology during ongoing endoscopy in full resolution by point scanning laser fluorescence analysis. Cellular, vascular and connective structures can be seen in detail. Graduation of cellular changes with endomicroscopy allows an immediate in-vivo diagnosis of different gastrointestinal diseases. The diagnostic spectrum of confocal endomicroscopy is currently expanding from screening and surveillance for colorectal cancer towards Barrett's esophagus, Helicobacter pylori associated gastritis and early gastric cancer. The new detailed images seen with confocal laser endomicroscopy are unequivocally the beginning of a new era where this optical development will allow a unique look on cellular structures and functions at and below the surface of the gut.