Background: Small group teaching is an important part of undergraduate medical education, providing the ideal setting for learners to clarify misunderstandings, test hypotheses and evaluate ideas. Many schools undergoing curriculum reform have increased the time students spend in small group learning. However, there is an overall paucity of literature examining case-based small group sessions in medical school. Objective: This study was designed to examine student and facilitator perceptions of effective case-based small group teaching in the pre-clinical years and compare results in order to identify similarities and differences and identify key areas of disconnect so that the small group learning experience can be improved. Methods: An 18-item survey was emailed to all 388 students who had started the second year of medical school at the University of Massachusetts between August 2008 and August 2010 and to 146 of 161 facilitators who had facilitated a case-based small group session during that same time. Chi-square tests of equality of proportions were used to compare the answers of students and small group facilitators. Results: 79 (54%) small group facilitators and 195 (50%) students responded. Student and facilitator responses were similar in the areas regarding goals of small group sessions and responsibilities of the facilitator. Significant difference was noted between cohorts about the most important roles of the facilitator, whether facilitators and/or students should attend training prior to sessions, whether groups should follow a consistent format, how students should be expected to prepare for small groups, how student knowledge and performance should be assessed, and whether the small group leader should be a skilled facilitator or content expert. Conclusions: This study demonstrates that there are areas where perceptions of effectiveness differ between students and facilitators. Identifying these areas presents an opportunity to make small group sessions more effective by allowing for more informed facilitator development and better communication of session expectations to students. The lack of a substantive body of literature on this important trend in medical education, coupled with our findings, suggests that further study is needed to identify characteristics of case-based small group learning that are mutually valued by students and facilitators. This will encourage the development of small group sessions that are deemed effective and maximize learning and teaching time.