Provides information on the evolution and genomic organization of ultra-conserved non-coding elements (UCNEs) in multiple vertebrate species. UCNEbase currently covers 4,351 such elements in 18 different species. Around half of these elements are located within intergenic regions (2,139) and the rest are located within non-coding parts of genes: introns (1,713) and UTRs (499). The majority of UCNEs are supposed to be transcriptional regulators of key developmental genes. 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.