AAV genome size analysis  is usually performed by denaturing agarose-gel electrophoresis and southern blot. However, both techniques are time consuming and have limited resolution on determining sizes. Capillary electrophoresis with laser induced fluorescent (CE-LIF) has been developed recently as an alternative to provide fast and sensitive genome integrity analysis while offering high resolution size determination.³ Currently, AAV genome integrity analysis by CE-LIF is performed one sample at a time using the single-capillary system. Multiplexing the analysis can help decrease the analysis or profiling time for multiple serotypes or AAV vectors with different genome sizes. Presented here is genome integrity analysis using a multi-capillary system where parallel processing can be done with 8 capillaries in a single run. A direct comparison of the genome integrity analysis on the single capillary CE-LIF system and the multi-capillary system was performed showing similar data quality between the two systems. Percent corrected peak area values obtained with the two systems for intact genome and impurity peaks of different AAV samples were very consistent. With the multiplexing capability, quick assessment of the genome integrity of AAVs of different serotypes or different genome payloads can be achieved for up to 8 samples in a single run.  Additionally, good reproducibility was also obtained when 10 consecutive runs of RNA markers were carried out in parallel on the 8 capillary cartridge system. RSD of < 1% and < 5% were obtained for migration time and percent corrected peak area, respectively across 80 injections for all RNA markers.