Important progress has been made in the past two years in the identification of Pol II promoters. For most other regulatory elements, however, current biological knowledge is still insufficient to allow the development of prediction tools. The phylogenetic-footprinting strategy, which is based on the comparative analysis of homologous sequences, is a very efficient approach to identify new unknown regulatory elements. The recent organization of large-scale sequencing projects for some model vertebrate organisms will be extremely valuable for the prediction of regulatory elements in the human genome.