Confocal laser endomicroscopy (CLE) is a new endoscopic technique that allows in vivo real time histopathology. The method provides "optical" biopsies, giving the endoscopist the possibility of immediate interpretation and intervention. In colorectal cancer CLE has been used to distinguish neoplastic from non-neoplastic lesions. Lately, CLE has been used to monitor anti-angiogenic therapy by fluorescence labelled antibodies targeted against endothelial markers. The review describes CLE and the potential of the method in relation to colorectal polyps, cancer and inflammatory bowel disease.