Asymmetric flow field‐flow fractionation (AF4) is an analytical separation technique capable of providing information on different parameters of complex systems in a single measurement. Although it shows promise to be an important tool in the field of gene therapy, AF4 has only occasionally been used to study gene delivery vectors such as polyplexes. Here, AF4 is applied to investigate novel vector systems based on hybrid polymer–magnetic micelles, magnetopolyplexes. These are multicomponent systems, composed of small magnetic nanoparticles loaded in cationic block copolymer micelles that are complexed with DNA; they exhibit enhanced transfection efficiency in the presence of a magnetic field. It is demonstrated that the application of AF4 to these systems provides complementary information related to the fractionation of the samples, the disintegration of the vectors, the presence of fractions of small particles, unbound micelles, and DNA, and the composition of the magnetopolyplexes, which can hardly be obtained by conventional methods.