The department encompasses thirteen large research groups, each containing one or more full professors, as well as a number of associate and/or assistant professors. The research groups represent key organizational units within the department, and provide continuity within chosen research themes, as well as opportunities for sharing of infrastructure and short-term financial risks. As a major step towards the creation of research focus, the department has adopted a new organizational structure, where all research groups are now part of one or more research disciplines, also called 'clusters', namely FBS - Fluids, Bio and Soft Matter, PB - Plasmas and Beams and NQP - Nano, Quantum and Photonics. This new grouping has created a structure where, both physically and organizationally, research groups find themselves in the vicinity of the other research groups that they most intensively collaborate with, or would be most likely to.

In addition to the research groups and the three disciplines, the department manages a number of institutes and research centers that are operated jointly with other departments within TU/e or with external partners.