The main vector for gene therapy is adeno-associated virus (AAV), and a rapid, robust, and cost-effective full and empty capsid analysis method is needed during process development. While the gold standard is analytical ultracentrifugation (AUC), it is expensive, time-consuming, and poorly suited for high-throughput screening of conditions. Alternative methods with varying performance and cost do exist, but most necessitate pure, concentrated samples in large quantities for accurate results. Full and empty capsid separation can be achieved with ion exchange, by using a small difference in charge (full capsids generally have a lower pI than empty capsids). Previously, we have presented full and empty capsid preparative separation for AAV2, AAV5, AAV8, and AAV9 using Capto™ Q chromatography resin. Here, we showcase how Capto™ Q (HiTrap™ column, 1 mL) run on an ÄKTA pure™ 25 chromatography system can determine the percentage of full capsids of AAV8 and AAV9 in less than 5 minutes with minimal sample consumption.