Fluorescence molecular endoscopy has the potential to improve lesion identification, evaluate therapy response and image biological distribution of medications. The majority of research is performed in gastroenterology to identify polyps and (pre-) cancerous lesions or to evaluate therapy response after neoadjuvant chemoradiotherapy.1–8 However, for extensive use of this technique within the clinical field, standardization and quantification of the fluorescence signal is essential. Quantitative fluorescence molecular endoscopy (qFME) combines the best of two worlds. Wide-field fluorescence imaging allows for a general overview of the fluorescence signal and identifies regions of interest. This thesis investigates the optimalization and implementation of quantitative fluorescence molecular endoscopy into standard clinical care, with a focus on the three aforementioned clinical challenges. The first part of this thesis focusses on standardization of both wide-field fluorescence endoscopy and reflectance spectroscopy system, whereas the second part discusses the clinical application of quantitative fluorescence molecular endoscopy in multiple clinical fields.