Recent successes in forming different shaped face centered cubic (fcc) metal nanostructures has enabled a greater understanding of nanocrystal growth mechanisms. Here we extend this understanding to the synthesis of hexagonally close packed (hcp) metal nanostructures, to form uniquely faceted ruthenium nanocrystals with a well-defined hourglass shape. The hourglass nanocrystals are formed in a three-step thermodynamic growth process with dodecylamine as the organic stabilizer. The hourglass nanocrystals are then shown to readily self-assemble to form a new type of nanocrystal superlattice.