Real-time in vivo microscopic imaging has become a reality with the advent of confocal and nonlinear endomicroscopy. These devices are best utilized in conjunction with standard white light endoscopy. We evaluated the use of fluorescence endomicroscopy in detecting microscopic abnormalities in colonic tissues. Mice of C57bl/6 strain had intraperitoneal injection with azoxymethane once every week for five weeks and littermates, not exposed to azoxymethane served as controls. After 14 weeks, intestines were imaged by fluorescence endomicroscopy. The images show obvious cellular structural differences between those two groups of mice. The difference in endomicroscopy imaging can be used for identifying tissues suspicious for neoplasia or other changes, leading to early diagnosis of gastrointestinal track of cancer.