A flow fluorometric approach to study cationic lipoid–DNA complexes is presented. The approach uses standard flow cytometry equipment and common fluorescent dyes (BODIPY and ethidium homodimer-2) to detect both lipoid and DNA content in individual particles. In addition, a procedure that allows determination of whether or not liposomes remain intact is described. The procedure is based on monitoring the retention of a polar tracer that has been preloaded into its aqueous compartment. Sample preparation, instrument setup, data analysis, and methodological limitations are described. Applications of the procedure to cationic lipoid–DNA complexes are described, and illustrations are given for the determination of how the lipoid content, composition, and structure of individual lipoplexes in a population evolve over time, starting at about 1 min after DNA and vesicles are mixed. Analogous procedures can be applied to other heterogeneous particles and supramolecular structures.