Little comparative information is available on the detailed intracellular dynamics (diffusion, active movement, and distribution mechanisms) of nanoparticles (≤ 100 nm) and sub-micron particles (> 100 nm). Here, we quantitatively examined the intracellular movements of different-sized particles and of the endosomal vesicles containing those particles. We showed that silica nanoparticles of various sizes (30 to 100 nm) had greater motility than sub-micron particles in A549 cells. Although particles of different sizes localized in the early endosomes, late endosomes, and lysosomes in different proportions, their motilities did not vary, regardless of the vesicles in which they were localized. However, surprisingly, endosomal vesicles containing silica nanoparticles moved faster than those containing sub-micron particles. These results suggest that nanoparticles included within endosomal vesicles do not suppress the motility of the vesicles, whereas sub-micron particles perturb endosomal vesicle transport. Our data support a new hypothesis that differences in particle size influence membrane trafficking of endosomal vesicles.