A facile method is presented for preparation of dinucleoside pyrophosphate derivatives based on reaction of a nucleoside 5'-monophosphate with carbonyldiimidazole followed by treatment of the resulting nucleoside 5'-phosphoimidazolide with a nucleoside 5'-phosphate. This method is suitable for preparation of pyrophosphates analogous to NAD, FAD, and related natural pyrophosphates. The resulting compounds are useful for mechanistic studies of enzymes that use natural pyrophosphates as co-factors or substrates, and in development of inhibitors that have potential applications as therapeutic agents.