The partial transformation of ionic nanocrystals through cation exchange has been used to synthesize nanocrystal heterostructures. We demonstrate that the selectivity for cation exchange to take place at different facets of the nanocrystal plays an important role in determining the resulting morphology of the binary heterostructure. In the case of copper(I) (Cu+) cation exchange in cadmium sulfide (CdS) nanorods, the reaction starts preferentially at the ends of the nanorods such that copper sulfide (Cu2S) grows inward from either end. The resulting morphology is very different from the striped pattern obtained in our previous studies of silver(I) (Ag+) exchange in CdS nanorods where nonselective nucleation of silver sulfide (Ag2S) occurs (Robinson, R. D.; Sadtler, B.; Demchenko, D. O.; Erdonmez, C. K.; Wang, L.-W.; Alivisatos, A. P. Science 2007, 317, 355-358). From interface formation energies calculated for several models of epitaxial connections between CdS and Cu2S or Ag2S, we infer the relative stability of each interface during the nucleation and growth of Cu2S or Ag2S within the CdS nanorods. The epitaxial attachments of Cu2S to the end facets of CdS nanorods minimize the formation energy, making these interfaces stable throughout the exchange reaction. Additionally, as the two end facets of wurtzite CdS nanorods are crystallographically nonequivalent, asymmetric heterostructures can be produced.