A simple “stop think” approach was developed to encourage the self-assessment of learning. A key element was the requirement for students to rate their feeling of difficulty before [FOD_(pre)] and after [FOD_(post)] completing each of three authentic anatomy and physiology concept map exercises. The cohort was divided into low- (group L) and high-performing (group H) groups (based on final subject marks). Both FOD_(pre) (group L) and FOD_(post) (groups L and H) were significantly negatively correlated with score for some maps. A comparison of FOD_(pre) and FOD_(post) showed that students changed their mind about difficulty in 58–70% of the completed maps. Students who changed their estimation were asked to provide explanatory comments, and an increase in difficulty was related to problems with map link generation. For students who found the maps easier, 40% of comments indicated that map generation prompted recall of information from memory. Both difficulty estimations and comments supported the contention that students were self-assessing their interaction with the concept maps. Group H was significantly older than group L, had significantly higher levels of deep strategic and deep motivational learning, and had significantly higher marks in two of three concept map exercises. Notwithstanding these differences, the results from the “stop think” approach were similar between groups, indicating that it may be appropriate for students of varying academic ability. It is suggested that “stop think” may be a useful approach to encourage student self-assessment, an important step in assisting self-regulated learning development.