Most scientific research is judged based on the quality of controlled experiments and carefully analyzed results. In addition, proper levels of regulation in terms of biosafety and animal usage are a routine part of the scientific research process for laboratories. For many biologists, educational research is much more of a black box. While faculty have many great ideas on how to improve education, they struggle with the best way to evaluate whether their ideas lead to greater student outcomes. Here we provide a review of compliance issues related to educational research, as well as describe ways in which pedagogical innovations in biology can be assessed. We also describe some of the challenges related to educational research and how these could be addressed.