The cis-regulatory region of target genes is key elements in the transcriptional regulation of gene expression. Many of these cis-regulatory regions have not been identified by either biological experiments or computational methods. Recently, a few additional C2H2 zinc finger transcription factor binding sites have been discovered. The majority of the zinc finger binding sites, however, are still unknown. In this study, we used publically available data to evaluate possible interaction patterns between nucleotides and the amino acids of zinc finger domains. We calculated the most probable state path of three nucleotides sequences using a Hidden Markov Model (HMM). We used these computations to predict C2H2 zinc finger transcription factor binding sites in cis-regulatory regions of their target genes (http://bioinfo.hanyang.ac.kr/ZIFIBI/frameset.php). (c) 2008 Elsevier Inc. All rights reserved.