Identifying the phase purity of CdS nanorods (NRs) is complicated by the serious overlap between the X-ray diffraction peaks of zinc blende and wurtzite phases as well as anisotropic growth, which might hide a mixed phase. Here we show that the density gradient ultracentrifugation rate separation method can be used to sort CdS NRs synthesized under nitrogen according to differences in particle size and morphology. Furthermore, it was found that the different sized NRs formed in a single batch synthesis had different phases: the thinner ones (<3.5 nm in diameter) were predominantly wurtzite phase, while the thicker ones (>5 nm in diameter) were mainly zinc blende phase. Dark-field transmission electron microscopy (TEM) and high-resolution TEM images indicated the presence of numerous stacking faults in the thick zinc blende rods, while the wurtzite thin rods were exclusively single crystals. As a result of the differences in phase and stacking faults, the NRs showed different photoluminescent properties. The development of an effective way of separating such NRs thus leads to further insight into the differences in phase, structure, and optical properties between individual colloidal particles synthesized in a single batch. A preliminary mathematical model of the separation process has been proposed.