The predecessor of the department, the focal area Clinical Morphology and Biomedical Engineering (CMBE), was founded in 2005 by the Medical Faculty of the University Basel. Two endowed professorships were established, an assistant professorship sponsored by Hansjoerg Wyss, and an associate professorship sponsored by Thomas Straumann.
The newly generated highly collaborative environment resulted in numerous interdisciplinary clinical research projects that led to over 350 peer-reviewed publications and 30 book chapters (2005–2014). In 2014, the CMBE consisted of multiple externally founded research groups, inter alia:
- Hightech Research Center of Cranio-Maxillfacial Surgery (HFZ, Hans-Florian Zeilhofer)
- Biomaterials Science Center (BMC, Bert Müller)
- Center for medical Image Analysis & Navigation (CIAN, Philippe Cattin, former Medical Image Analysis Center)
- Gait Laboratory at UKBB (Reinald Brunner), and the
- Laboratory for Orthopedic Biomechanics and Micro-Calorimetriy (LOB). In 2013, the LOB was re-structured into the Center of Biomechanics (COB), which collaborates with multiple clinical professorships at various clinical institutions.
In 2015, the new Department of Biomedical Engineering (DBE) has been opened in Allschwil with the aim to further advance procedures and technologies for medical treatment. The core of the new department is composed of the former CMBE research groups and meanwhile consists of roughly 70 researchers in Allschwil and around 60 medical doctors from the University Hospital Basel and the University Children's Hospital Basel.