Poly(ethylene imine) (PEI) is an established non-viral vector system for the delivery of various nucleic acids in gene therapy applications. Polyelectrolyte complexes between both compounds, so called polyplexes, are formed by electrostatic interactions of oppositely charged macromolecules and are thought to facilitate uptake into cells. Such complexes form spontaneously and on lab scale they are usually prepared by mixing solutions through pipetting. Hence, an optimized preparation procedure allowing the scale-up of well-defined polyplexes would be of general interest. We developed a new method for microfluidic polyplex preparation on a chip. The mixing behaviour within the microfluidic channels was evaluated. Polyplexes with PEI and plasmid DNA were prepared using this method, in comparison to the standard pipetting procedure. Sizes and polydispersity indices of these complexes were examined. The influence of various parameters on the polyplex characteristics and the suitability of this production procedure for other PEI-based complexes were also evaluated. It was shown that polyplexes could easily be prepared by microfluidics. The ratio of PEI to DNA was most important for the formation of small polyplexes, whereas other parameters had minor influence. The size of polyplexes prepared with this new method was observed to be relatively constant between 140 nm and 160 nm over a wide range of complex concentrations. In comparison, the size of polyplexes prepared by pipetting (approximately 90 nm to 160 nm) varied considerably. The versatility of this system was demonstrated with different (targeted) PEI-based vectors for the formation of complexes with pDNA and siRNA. In conclusion, polyplex preparation using microfluidics could be a promising alternative to the standard pipetting method due to its suitability for preparation of well-defined complexes with different compositions over a wide range of concentrations.