Three-prime untranslated regions (3'UTRs) are widely recognized as important post-transcriptional regulatory regions of mRNAs. RNA-binding proteins and small non-coding RNAs such as microRNAs (miRNAs) bind to functional elements within 3'UTRs to influence mRNA stability, translation and localization. These interactions play many important roles in development, metabolism and disease. However, even in the most well-annotated metazoan genomes, 3'UTRs and their functional elements are not well defined. Comprehensive and accurate genome-wide annotation of 3'UTRs and their functional elements is thus critical. We have developed an open-access database, available at http://www.UTRome.org, to provide a rich and comprehensive resource for 3'UTR biology in the well-characterized, experimentally tractable model system Caenorhabditis elegans. UTRome.org combines data from public repositories and a large-scale effort we are undertaking to characterize 3'UTRs and their functional elements in C. elegans, including 3'UTR sequences, graphical displays, predicted and validated functional elements, secondary structure predictions and detailed data from our cloning pipeline. UTRome.org will grow substantially over time to encompass individual 3'UTR isoforms for the majority of genes, new and revised functional elements, and in vivo data on 3'UTR function as they become available. The UTRome database thus represents a powerful tool to better understand the biology of 3'UTRs.