One of the major proceedings in the field of gastrointestinal endoscopy has been the advent of molecular imaging, which possesses the potential to have a significant effect on the existing diagnostic and therapeutic paradigms. Molecular imaging encompasses different methods that enable the visualization of disease-specific morphologic or functional alterations of the mucosa based on the molecular signature of individual cells. This development has been made possible by advancements in basic science coupled with technological innovations in endoscopy, both facilitating the identification and characterization of mucosal lesions in vivo based on the lesions’ molecular composition rather than their morphologic structure alone. Novel studies based on fluorescent antibody imaging pave the road toward clinical translation and give hope for improved diagnosis and targeted therapies in gastrointestinal diseases.