Objectives: Traditional anatomy education involves theoretical lectures and practical applications, including examination of cadavers and models. In recent years, new technologies in biomedical fields have included three-dimensional (3D) modeling techniques that enable rapid creation of a 3D computer version of physical models. Such 3D modeling can be used as an active educational tool that enables students to better understand organs and how these organs are positioned relative to one another in anatomy education. The aim of this study was to analyze how the active role and involvement of students in 3D modeling contributes to anatomy education and 3D thinking.Methods: In this study, 29 Term II students studying in the Baflkent University School of Medicine were enrolled with 3D modeling training based on an anonymized CT sample. In addition to defining anatomic structures observed in the sections, 3D images of the common carotid artery, thyroid gland and trachea were obtained using the TT3D-BMMP software, and the position of these structures relative to one another was evaluated. The results of the anatomy quizzes given before and after the 3D modeling training were statistically evaluated.Results: A statistically significant difference was found between the results of the quizzes administered before and after the training (p<0.001). However, no statistically significant difference was found between male and female students in terms of the quiz results before training, while a significant difference was found in the quiz results after training. Conclusion:We believe that sectional and radiological identification and recognition of anatomical structures by the students through 3D modeling will facilitate their anatomy education and be beneficial in terms of clinical practices in the future.