Disclosed are nanocrystals comprising metals and metal alloys, which are formed by a process that results in a layer of graphite in direct contact with the metallic core. The nanocrystals may be used in vivo as MRI contrast agents, X-ray contrast agents, near IR (NIR) heating agents, drug delivery, protein separation, catalysis etc. The nanocrystals may be further functionalized with a hydrophilic coating, e.g., phospholipid-polyethylene glycol, which improves in vivo stability. The process comprises chemical vapor deposition of metals adsorbed onto silica as a fine powder, in conjunction with a carbon containing gas, which coats the metal particles. The silica is then etched away. Preferred metals include iron, gold, cobalt, platinum, ruthenium and mixtures thereof, e.g., FeCo and AuFe. The process permits control of the alloy compositions, size, and other characteristics.