Introduction: An objective of undergraduate medical education is to teach students how to think like physicians through a process called clinical reasoning. Currently, clerkship directors often feel that students enter their clinical years with a marginal comprehension of clinical reasoning concepts; instruction in this area could be improved. Although there have been previous educational studies assessing curricular interventions to improve the instruction of clinical reasoning, it is not yet known what happens at an individual level between an instructor and a small group of students in the teaching of clinical reasoning. This research will identify how clinical reasoning is being taught in a longitudinal clinical reasoning course. Methods: The Introduction to Clinical Reasoning course is a 15-month-long case-based course held in the preclinical curriculum of the USU. Individual sessions involve small-group learning with approximately seven students per group. Throughout the academic year of 2018-2019, 10 of these sessions were videotaped and transcribed. All participants provided informed consent. A thematic analysis was performed using a constant comparative approach. Transcripts were analyzed until thematic sufficiency was reached. Results: Over 300 pages of text were analyzed; new themes ceased to be identified after the eighth session. Topics included obstetrics, general pediatric issues, jaundice, and chest pain; these sessions were taught either by attendings, fellows, or fourth-year medical students with attending supervision. The thematic analysis revealed themes associated with clinical reasoning processes, themes associated with knowledge organization, and a theme associated with clinical reasoning in the military. The clinical reasoning process themes included problem list construction and refinement, differential diagnosis, naming and defending a leading diagnosis, and clinical reasoning heuristics. The knowledge organization themes included illness script development and refinement and semantic competence. The final theme was military relevant care. Conclusions: In individual teaching sessions, preceptors emphasized problem lists, differential diagnoses, and leading diagnoses in a course designed to strengthen diagnostic reasoning in preclerkship medical students. The use of illness scripts was more often implicitly used rather than explicitly stated, and students used these sessions to use and apply new vocabularies related to a clinical presentation. Instruction in clinical reasoning could be improved by encouraging faculty to provide further context to their thinking, by encouraging the comparing and contrasting of illness scripts, and by using a shared vocabulary for clinical reasoning. Limitations of this study include that it was done in the context of a clinical reasoning course and that it was done at a military medical school, which may limit generalizability. Future studies could determine if faculty development could improve the frequency of references to the clinical reasoning processes that could improve student readiness for clerkship.