This study evaluates the biodistribution of adeno-associated virus type 9 (AAV9) encoding the enhanced green fluorescence protein (EGFP) gene in the mouse brain and peripheral organs following intranasal (IN) or intravenous (IV) AAV9 administration. Droplet digital polymerase chain reaction (ddPCR) and an enzyme-linked immunosorbent assay (ELISA) were employed to quantify the EGFP transgene DNA copies and protein concentrations, respectively, in the harvested brains and peripheral organs of Cr.NIH (Swiss), BALB/c, and C57BL/6J mice four weeks post-IN or IV delivery. Multiple mice strains were included in this study to validate delivery across diverse genetic backgrounds. DNA copy numbers and protein concentrations were compared between the two delivery routes to evaluate the delivery efficiency and spatial distribution of IN AAV administration relative to the conventional IV delivery method.