The structural organization of research facilities within a surgical university center should aim at strengthening the department's research output and likewise provide opportunities for the scientific education of academic surgeons. We suggest a model in which several independent research groups within a surgical department engage in research projects covering various aspects of surgically relevant basic, translational or clinical research. In order to enhance the translational aspects of surgical research, a permanent link needs to be established between the department's scientific research projects and its chief interests in clinical patient care. Importantly, a focus needs to be placed on obtaining evidence-based data to judge the efficacy of novel diagnostic and treatment concepts. Integration of modern technologies from the fields of physics, computer science and molecular medicine into surgical research necessitates cooperation with external research facilities, which can be strengthened by coordinated support programs offered by research funding institutions.