Eukaryotic regulatory regions have been studied extensively due to their importance for gene regulation in higher eukaryotes. However, the understanding of their organization is clearly incomplete. In particular, we lack accurate in silico methods for their prediction. Here we present a new HMM-based method for the prediction of regulatory regions in eukaryotic genomes using position weight matrices of the relevant transcription factors. The method reveals and then utilizes the regulatory region structure (preferred binding site arrangements) to increase the quality of the prediction, as well as to provide a new knowledge of the regulatory region organization. We show that our method can be successfully used for the identification of regulatory regions in eukaryotic genomes with a quality higher than that of other methods. We also demonstrate the ability of our algorithm to reveal structural features of the regulatory regions, which could be helpful for the deciphering of the transcriptional regulation mechanisms in higher eukaryotes.