Polycations like poly(ethylene imine) (PEI) or poly(L-lysine) (pLL) form nanometer-sized complexes with nucleic acids (polyplexes) which can be used for gene delivery. It is known that the properties of these -carriers can be greatly improved by introducing disulfide bridges on the polymers, thus making them reduction sensitive. However, little is known about how such modified carriers behave intracellularly. Here, we describe a method that uses the reduction-sensitive fluorescent dye BODIPY FL L-cystine to label PEI and pLL. Our probe is activated under reductive conditions leading to strongly increased fluorescence intensity. Subsequently, we show how the intracellular route of polyplexes made from these labeled polymers can be monitored by flow cytometry.