The crucial role of the non-coding portion of genomes is now widely acknowledged. In particular, mRNA untranslated regions are involved in many post-transcriptional regulatory pathways that control mRNA localisation, stability and translation efficiency. A review is given of the most recent research works on the functional characterisation of eukaryotic mRNA untranslated regions. In order to make possible a systematic and detailed sequence analysis of mRNA untranslated regions (UTRs), a non-redundant database of metazoan mRNA untranslated sequences annotated for the occurrence of specific functional elements, UTRdb, was devised. These elements, whose consensus structure has been devised on the basis of experimental assays and of comparative analyses, have been collected in the UTRsite database. A suitable pattern-matching software has been devised to search UTRsite patterns in user-submitted sequences, also assessing their statistical significance. Structural, compositional and evolutionary features of untranslated sequences of metazoan mRNAs have been investigated showing peculiar intra- and interspecific patterns.