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Purpose Hypothetico-deductive reasoning (HDR) is an essential learning activity and a learning outcome in problem-based learning (PBL). It is important for medical students to engage in the HDR process through argumentation during their small group discussions in PBL. This study aimed to analyze the quality of preclinical medical students' argumentation according to each phase of HDR in PBL. Methods Participants were 15 first-year preclinical students divided into two small groups. A set of three 2-hour discussion sessions from each of the two groups during a 1-week-long PBL unit on the cardiovascular system was audio-recorded. The arguments constructed by the students were analyzed using a coding scheme, which included four types of argumentation (Type 0: incomplete, Type 1: claim only, Type 2: claim with data, and Type 3: claim with data and warrant). The mean frequency of each type of argumentation according to each HDR phase across the two small groups was calculated. Results During small group discussions, Type 1 arguments were generated most often (frequency=120.5, 43%), whereas the least common were Type 3 arguments (frequency=24.5, 8.7%) among the four types of arguments. Conclusion The results of this study revealed that the students predominantly made claims without proper justifications; they often omitted data for supporting their claims or did not provide warrants to connect the claims and data. The findings suggest instructional interventions to enhance the quality of medical students' arguments in PBL, including promoting students' comprehension of the structure of argumentation for HDR processes and questioning.