The size-dependent Kirkendall effect is studied by using Co nanoparticles. The sizes of Co nanoparticles differing by their crystal structures called nanocrystallinity, namely amorphous, polycrystalline fcc, single crystalline hcp, and single crystalline epsilon phase, are modulated from 4 to 10 nm. The nanoparticles self-assembled in 2D superlattices and differing by their nanocrystallinities are subjected to oxygen at 200 degrees C for 10 min. With single-domain nanocrystals differing by their crystalline structure (e and hcp phases), marked changes in the final structures are observed: upon increasing the nanocrystal size, the epsilon phase favors formation of a hollow structure whereas a transition from single-domain hollow to multidomain core/shell structures takes place with the hcp phase. With polycrystalline fcc Co nanocrystals, a transition from a hollow to a yolk/shell structure is observed, whereas with amorphous cobalt, solid CoO nanoparticles are produced at the smaller size and are converted to the core/shell structure at the larger one. These differences in size effect are attributed to the change in the control of the inward flow of oxygen atoms and the outward flow of Co atoms with the crystalline structure of cobalt nanoparticles. Such a diffusion process described here on the Kirkendall effect can be studied for other metal nanocrystals.