Cell-mediated nanoparticle delivery has recently emerged as an efficacious method of delivering therapeutic agents across physiological barriers. Use of cells as nanodelivery vehicles requires accurate assessment of their loading capacity and identification of intracellular compartments where nanoparticles are sequestered. This is of great interest since specific endocytic trafficking routes can ultimately influence the mode of nanoparticle release and their efficacy and function. Here, we describe a technique that allows for the isolation of individual populations of nanoparticle-containing endosomes for subsequent quantitative analysis and more accurate description of where nanoparticles are stored on a subcellular level.