To seek longitudinal changes in metacognitive processes through problem-based learning (PBL), we analysed the contents of all comments written reflectively by the third-year students after they finished discussions in each PBL session. After dividing their comments into meaningful units, we focused on two major thematic categories and five sub-categories to be analysed. 1) The number of units decreased significantly (chi-square: p=0.02). 2) Only the proportion of units categorised as “comprehension” in “individual learning” showed significant increase (Bonferroni: p<0.001). 3) Comments in this category stated that “I don't understand so-and-so.” 4) The increase of “comprehension” as they experienced more PBL suggested that students' knowledge of ignorance as metacognition was fostered through sessions in medical PBL.