A myriad of cationic polymeric delivery vehicles are currently being developed with the aim of transporting various forms of nucleic acids to mammalian cells. The complexes between polycations and nucleic acids are referred to as polyplexes. The screening for successful polyplex candidates requires interdisciplinary research platforms and techniques for a more profound understanding of biophysical properties of delivery vehicles and their biological performance, including stability, transfection efficacy and possible cytotoxicity. Fluorescent microscopy has proven to be a useful tool for real-time monitoring of performance and intracellular trafficking of polyplexes as well as for assessing cell functionality. This review highlights the application of some of the most promising fluorescent microscopy platforms in relation to polyplex-mediated transfection processes.