ABSTRACT Introduction Research in the field of medical reasoning has shed light on the reasoning process used by medical students. The strategies in this process are related to the analytical [hypothetical-deductive (HD)] and nonanalytic [scheme-inductive) (SI)] systems, and pattern recognition (PR)]. Objective To explore the clinical reasoning process of students from the fifth year of medical school at the end of the clinical cycle of medical internship, and to identify the strategies used in preparing diagnostic hypotheses, knowledge organization and content. Method Qualitative research conducted in 2014 at a Brazilian public university with medical interns. Following Stamm’s method, a case in internal medicine (IM) was built based on the theory of prototypes (Group 1 = 47 interns), in which the interns listed, according to their own perceptions, the signs, symptoms, syndromes, and diseases typical of internal medicine. This case was used for evaluating the clinical reasoning process of Group 2 (30 students = simple random sample) obtained with the “think aloud” process. The verbalizations were transcribed and evaluated by Bardin’s thematic analysis. The content analysis were approved by two experts at the beginning and at the end of the analysis process. Results The interns developed 164 primary and secondary hypotheses when solving the case. The SI strategy prevailed with 48.8%, followed by PR (35.4%), HD (12.2%), and mixed (1.8 % each: SI + HD and HD + PR). The students built 146 distinct semantic axes, resulting in an average of 4.8/participant. During the analysis, 438 interpretation processes were executed (average of 14.6/participant), and 124 combination processes (average of 4.1/participant). Conclusions The nonanalytic strategies prevailed with the PR being the most used in the development of primary hypotheses (46.8%) and the SI in secondary hypotheses (93%). The interns showed a strong semantic network and did three and a half times more interpretation than combination processes, reflecting less deep organization and content of knowledge when compared with experienced physicians.