One of the more common uses of the program FingerPrint Contigs (FPC) is to assemble random restriction digest fingerprints of overlapping genomic clones into contigs. To improve the rate of assembling contigs from large fingerprint databases we have adapted FPC so that it can be run in parallel on multiple processors and servers. The current version of parallelized FPC has been used in our laboratory to assemble mammalian BAC fingerprint databases, each containing more than 300000 BAC fingerprints.