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This study aimed to assess the perception of PBL among Japanese medical students.Learning effects and challenges of PBL from the students' viewpoint were assessed with an exploratory sequential mixed method. Focus group discussions followed by thematic analysis were conducted with 27 students and residents. Then a questionnaire survey was carried out. A total of 119 out of 258 students (46.1%) responded. The results from 24 questions were analyzed with a residual analysis.Thematic analysis extracted 14 themes from four discussion topics. The participants in focus group discussion regarded the PBL program as a better learning method than lectures. But some key phrases on the challenge of social interaction, including reluctance to actively discuss and collaborate with unfamiliar peers, were found. The questionnaire survey revealed a significantly lower adjusted standardized residual (ASR) for the positive response in five of six questions in the category of social interaction; improvement of communication skills (ASR = -3.303, n = 118, p.001), enhancement of responsibility at group discussions (ASR = -2.078, n = 119, p = .038), building social networking (ASR = -3.006, n = 119, p = .003), becoming to sympathize with patients (ASR = -2.449, n = 119, p = .014) and understanding social aspects of clinical practice (ASR = -5.790, n = 119, p.001). Conclusion: The Japanese medical students perceived PBL as an effective learning strategy. However, they had a problem with social interactions.