Embryology is often difficult to teach because of the rapid, three-dimensional changes that occur simultaneously on a microscopic scale. A knowledge of normal and abnormal human development is important for understanding the pathophysiology, clinical treatment and surgical repair of mal formations. In this study, we developed a method to enhance the comprehension of human embryology and its associated malformations. The strategy used macro- and microscopical digital documentation of embryos, fetuses and neonates undergoing autopsy in the Department of Anatomical Pathology at the State University of Campinas. The images acquired were used in the Human Morpho-Physiology course of the university’s medical curriculum. The embryology lectures were divided into two parts. In the first part, the development of the body’s structures was explained, while in the second, macro- and microscopic images of selected autopsies were shown to the students, who were also encouraged to find and discuss the malformations and their clinical history, diagnosis and therapeutics. At the end of the course, the teaching material and the method used were evaluated using a questionnaire, interviews, and a test of the knowledge acquired during the lectures. Most of the students approved the method, and emphasized the importance of integration between basic and clinical disciplines. Their performance in the examination was also good.