Biophotonics encompasses the fundamental interactions of light and biological materials. The field has produced optical imaging, diagnostic and therapeutic devices that have impacted modern medicine. It has provided major advances in biomedical research through development of technologies for high resolution microscopy, and contributed to the progress in molecular labelling through the development of fluorescent proteins, and medically relevant contrast and therapeutic agents. Many of these interdisciplinary activities have involved bioengineers and have grown out of bioengineering departments. This special issue of ABME encompasses research papers at the interface of biophotonics and bioengineering which we have solicited from internationally renowned researchers. This includes a total of 16 review articles to introduce the field to a general audience of bioengineers, and the topics have been selected to cover a broad range of biophotonics research areas. The subjects of endoscopy and tissue optics are covered in reviews by Stoyanov on how computational