This article describes a systematic study of the nucleation and growth of Ag (and Au) on Pd nanocrystal seeds. By carefully controlling the reaction kinetics, the newly formed Ag atoms could be directed to selectively nucleate and then epitaxially grow on a specific number (ranging from one to six) of the six faces on a cubic Pd seed, leading to the formation of bimetallic nanocrystals with a variety of different structures. In addition to changing the injection rate of precursor, we also systematically investigated other reaction parameters including the capping agent, reductant, and reaction temperature. Our results suggest that the site-selective growth of Ag on cubic Pd seeds could be readily realized by optimizing these reaction parameters. On the basis of the positions of Pd seeds inside the bimetallic nanocrystals as revealed by TEM imaging and elemental mapping, we could identify the exact growth pathways and achieve a clear and thorough understanding of the mechanisms. We have successfully applied the same strategy based on kinetic control to cubic Pd seeds with different sizes and octahedral Pd seeds of one size to generate an array of novel bimetallic nanocrystals with well-controlled structures. With cubic Pd seeds as an example, we have also extended this strategy to the Pd-Au system. We believe this work will provide a promising route to the fabrication of bimetallic nanocrystals with novel structures and properties for applications in plasmonics, catalysis, and other areas.