Molecular imaging is a novel field in gastroenterology that uses fluorescently labelled probes to specifically highlight neoplastic lesions on the basis of their molecular signature. The development of molecular imaging has been driven by the need to improve endoscopic diagnosis and by progress in targeted therapies in gastrointestinal oncology to provide individualized treatment, which coincides with progress in endoscopy techniques and further miniaturization of detection devices. Different exogenous molecular probes for imaging include labelled antibodies, oligopeptides, affibodies(™) (Affibody AB, Bromma, Sweden), aptamers and activatable probes. Molecular imaging has been evaluated in two major indications: many trials have studied molecular imaging as a red flag technique to improve detection of lesions in wide-field imaging; on the other hand, microscopic analysis has been investigated for in vivo characterization of the molecular fingerprint of tumours with the ultimate goal of assessing the likelihood of response to targeted therapy. This Review focusses on the applications of molecular imaging that have immediate potential for translational science or imminent transition into clinical practice of gastrointestinal endoscopy.