Combining a professional development course on diagnostic endoscopy from SPIE (the international society advancing light-based research) and the authors’ graduate course on biomedical optics, this work is written for researchers in medical optics and biomedical engineering as well as graduate medical optics students. It uses extensive examples/case studies to familiarize readers with the basics of endoscopic optics, the pros and cons of white light endoscopy and fluorescence endoscopy for diagnostic applications, and various microscopic endoscopy imaging modalities. It covers basic optics, details of design and biomedical uses, as well as microscopic endoscopy, and endoscopic spectroscopy.