We conducted this study to investigate the effects of additional education using 3D visualization (3DV) and 3D printing (3DP) after applying 2D images for anatomical education in normal pediatric structures and congenital anomalies. For the production of 3DV and 3DP of the anatomical structures, computed tomography (CT) images of the four topics (the normal upper/lower abdomen, choledochal cyst, and imperforate anus) were used. Anatomical self-education and tests were administered to a total of 15 third-year medical students with these modules. Following the tests, surveys were conducted in order to evaluate satisfaction from students. In all four topics, there were significant increases in the test results with additional education with 3DV after initial self-study with CT (P< 0.05). The difference in scores was highest for the imperforate anus when 3DV supplemented the self-education. In the survey on the teaching modules, the overall satisfaction scores for 3DV and 3DP were 4.3 and 4.0 out of 5, respectively. When 3DV was added to pediatric abdominal anatomical education, we found an enhancement in understanding of normal structures and congenital anomalies. We can expect the application of 3D materials to become more widely used in anatomical education in various fields.