Most of the research on case-based science teaching at the university level involves comparative studies, which contrast student perceptions of case-based science teaching with more traditional teaching. Sometimes this type of research is being done to convince colleagues that case-based science teaching is equally effective if not better than traditional teaching. In this article, the authors present three examples, wherein they illustrate some problems with comparative studies that are not well controlled for instructor bias, not well planned to measure particular outcomes and have such weak interventions they yield data impossible to interpret. They present future questions worth investigating using classroom research. (For Part I, see EJ752581.)