The Graduate Program in Surgery founded in 1971 is the only program offering Master and Doctoral courses. At first, the program prioritized the high technical specialization in the surgical subareas, including experimental surgery. However, the program began to be offered to medical and non-medical specialists to provide academic training, especially in research with a translational approach in the surgical area. The incorporation of the area of Anatomy in the Department of Surgery substantially supported the implementation of the Translational view of the research. 

There are currently eleven lines of research, distributed in two areas of concentration: Surgery, which involves research and innovation projects related to clinical-surgical activities, with emphasis on critical analysis of access, diagnostic, and therapeutic processes, and Morphology and Experimental Medicine, with experimental projects and studies involving tissues, human, and animal body fluids, but mainly developed by non-medical researchers. This arrangement has enabled a close interaction between Applied Science and Basic Science for the quality of research. In 2020, the Critical Patient Assessment and Care research line was created due to the presence of professionals working in the intensive care sector, which is linked to the Department of Surgery and Anatomy.  This line comprises the interface of the surgical areas with the critical patient, in addition to the search for better care of the severe patient, as in the COVID pandemic.