Chromatin immunoprecipitation followed by sequencing with next-generation technologies (ChIP-Seq) has become the de facto standard for building genome-wide maps of regions bound by a given transcription factor (TF). The regions identified, however, have to be further analyzed to determine the actual DNA-binding sites for the TF, as well as sites for other TFs belonging to the same TF complex or in general co-operating or interacting with it in transcription regulation. PscanChIP is a web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria. PscanChIP can successfully identify not only the actual binding sites for the TF investigated by a ChIP-Seq experiment but also secondary motifs corresponding to other TFs that tend to bind the same regions, and, if present, precise positional correlations among their respective sites. The web interface is free for use, and there is no login requirement. It is available at http://www.beaconlab.it/pscan_chip_dev.