Molecular Systems Engineering (MSE) is a National Centre of Competence in Research (NCCR) funded by the Swiss National Science Foundation (SNSF), and headed by the University of Basel and the ETH Zurich. This NCCR combines expertise from chemistry, biology, physics, bioinformatics, and engineering. The overreaching aim is to develop tools and devices to monitor and manipulate off-equilibrium (bio)chemical systems. These may find applications in the synthesis of high added-value products, as innovative diagnostic tools and for the restoration of a desired cellular or organ function.NCCR MSE is at the forefront of the emerging field of molecular systems engineering, and has the potential of leading to a long-term paradigm shift in molecular sciences and a new structure of the Swiss research landscape.