Purpose To evaluate perceptions of fifth-year dental students' towards case-based orthodontic education. Methods The sample population consisted of 108 final year dental students (39 men, 69 women) who volunteered to participate in the project during their orthodontic clinical internship. Patient files including extraoral, intraoral photographs, hand-wrist, panoramic and cephalometric radiographs were randomly distributed. Each group presented their evaluations after 1 week. At the end of case discussions, students were given a questionnaire regarding their perceptions of case-based education. Differences in mean scores between groups were compared by independent samples t-test. Results The response rate was 100%. The majority of students strongly agreed that their interest and ability to interpret and diagnose the orthodontic data were increased. More than 60% strongly agreed that this education had a positive effect on their attention and effective learning. More than 45% strongly agreed that their communication with colleagues was increased, and women were significantly more inclined to group work than men (p < 0.05). More than 45% declared no additional burden. Conclusions Orthodontic case-based education was well received by final year dental students. The most noted improvement was observed in motivation, ability to comment on the diagnosis and treatment planning of orthodontic cases, without feeling an extra workload.