The purpose of this project was to develop Web-based learning modules that combine (1) animated 3D graphics; (2) 3D models that a student can manipulate independently; (3) passage of time in embryonic development; and (4) animated 2D graphics, including 2D cross-sections that represent different “slices” of the embryo, and animate in parallel. These elements were presented in two tutorials, one depicting embryonic folding and the other showing development of the nervous system after neural tube formation. The goal was to enhance the traditional teaching format—lecture combined with printed diagrams, text, and existing computer animations—with customized, guided, Web-based learning modules that surpassed existing resources. To assess module effectiveness, we compared quiz performance of control groups who attended lecture and did not use a supporting module, with study groups who used a module in addition to attending lecture. We also assessed our students' long-term retention of the material, comparing classes who had used the module with students from a previous year that had not seen the module. Our data analysis suggests that students who used a module performed better than those given only traditional resources if they used the module after they were already somewhat familiar with the material. The findings suggest that our modules—and possibly computer-assisted-instruction modules in general—are more useful if used toward the later stages of learning, rather than as an initial resource. Furthermore, our data suggest that the animation aids in long-term retention. Both medical students at the University of Cincinnati and medical faculty from across the country commented favorably on their experiences with the embryonic development modules. Anat Sci Ed 1:252–257, 2008. © 2008 American Association of Anatomists.