Locating transcription factor binding sites in genomic sequences is a key step in deciphering transcription networks. Currently available software for site search is mostly server-based, limiting the range and flexibility of this type of analysis. xFITOM is a fully customizable program for locating binding sites in genomic sequences written in C++. Through an easy-to-use interface, xFITOM that allows users an unprecedented degree of flexibility in site search. Among other features,it enables users to define motifs by mixing real sites and IUPAC consensus sequences,to search the annotated sequences of unfinished genomes and to choose among 11 different search algorithms.