UCNEbase (http://ccg.vital-it.ch/UCNEbase) is a free, web-accessible information resource on the evolution and genomic organization of ultra-conserved non-coding elements (UCNEs). It currently covers 4351 such elements in 18 different species. The majority of UCNEs are supposed to be transcriptional regulators of key developmental genes. As most of them occur as clusters near potential target genes, the database is organized along two hierarchical levels: individual UCNEs and ultra-conserved genomic regulatory blocks (UGRBs). UCNEbase introduces a coherent nomenclature for UCNEs reflecting their respective associations with likely target genes. Orthologous and paralogous UCNEs share components of their names and are systematically cross-linked. Detailed synteny maps between the human and other genomes are provided for all UGRBs. UCNEbase is managed by a relational database system and can be accessed by a variety of web-based query pages. As it relies on the UCSC genome browser as visualization platform, a large part of its data content is also available as browser viewable custom track files. UCNEbase is potentially useful to any computational, experimental or evolutionary biologist interested in conserved non-coding DNA elements in vertebrates.