Centrifugation is an increasingly important technique for nanomaterial processing. Here, we examine this process for gold, cadmium selenide, and iron oxide nanocrystals using an analytical ultracentrifuge. Such data provide an accurate measure of the sedimentation coefficients for these materials, and we find that this parameter has a significant dependence on the size and surface coating. Conventional models for particle sedimentation cannot capture the behavior of these nanocrystals unless the density of the nanocrystals is described by a size-dependent term that accounts for both the inorganic core and the organic coating. Using this modification in the particle sedimentation framework, it is possible to estimate sedimentation coefficients from information about the nanocrystal core and surface coating dimensions. Such data are useful in choosing the speeds for a centrifugation process and are particularly important when bimodal nanocrystal distributions are present.