Abstract: ABSTRACT: BACKGROUND: Non-coding RNAs (ncRNAs) are in emerging focus for both computational analysis and experimental research resulting in a growing number of novel, non-protein coding transcripts with often unknown functions. Whole genome screens in higher eukaryotes, for instance, provided evidence for a surprisingly large number of ncRNAs. To supplement these searches, we performed a computational analysis of seven yeast species and searched for new ncRNAs and RNA motifs. RESULTS: A comparative analysis of the genomes of seven yeast species yields roughly 2800 genomic loci that show the hallmarks of evolutionary conserved RNA secondary structures. 74% of these regions overlap with annotated non-coding or coding genes in yeast. Coding sequences that carry predicted structured RNA elements belong to a limited number of groups with common functions, suggesting that these RNA elements are involved in post-transcriptional regulation and/or cellular localization. About 70% of conserved RNA structures are found outside annotated coding sequences and known ncRNA genes. Many of these predicted elements overlap with UTR regions of particular classes of protein coding genes. In addition, a number of RNA elements overlap with previously characterized antisense transcripts. Transcription of about 120 predicted elements located in promotor regions and other, previously un-annotated, intergenic regions is supported by tiling array experiments, ESTs, or SAGE data. CONCLUSIONS: Our computational predictions strongly suggest that yeasts harbour a substantial pool of several hundred novel ncRNAs. In addition, we described a large number of RNA structures in coding sequences and also within antisense transcripts that were previously characterized using tiling arrays.