Computational Fluid Dynamics (CFD) is presented as a powerful tool to support design and optimization of microfluidic reactors. This is demonstrated by means of three case studies. First a three-dimensional scaffold for tissue engineering purposes is investigated using a combination of CFD and a simple biological model. The result is a suggestion of an improved geometry design. In the second case study a microfluidic cartridge of a novel automated in vitro fertilization device is presented, where the CFD model has supported the fluidic design of the microfluidic network in which the stem cells are grown. In the last case study a biocatalytic microfluidic reactor design is presented in which the material characteristics of substrates and products of the catalytic reaction can be investigated. As model system the transaminase catalyzed formation of methylbenzylamine (MBA) from acetophenone is investigated and it is demonstrated how the experimental investigation along with the CFD model can be used for the characterisation of the performance of the reactor system.