Gene therapy vectors such as plasmids, viruses (adeno-associated virus, lentivirus, etc.) and lipid nanoparticles featuring long-term expression of the transgene and excellent disease correction history are the most widely used delivery vehicles for medical treatment using genes to cure illness. During vector production, several quality control (QC) parameters should be closely monitored to comply with clinical safety and efficacy requirements. Current gene delivery vector manufacturing technologies, however, can neither guarantee the generation of the integrity of the plasmid or the transgene, neither having only full capsids/nanoparticles. Therefore, nicked and/or linear plasmids, partially filled and empty delivery vectors can also be part of the product, decreasing in this way the efficacy and safety upon clinical translation. Transgene integrity and nucleic acid impurities, on the other hand, may also represent a problem in the final product with therapeutic use of viral vectors, therefore, their analysis is of high importance as well. This presentation introduces a multi-attribute workflow for the analysis of gene delivery vectors using various modes of capillary electrophoresis, including capillary gel electrophoresis, CE-SDS, and capillary isoelectric focusing for plasmid purity, capsid protein, full/empty ratio and genome integrity analysis.