Polyadenylation of 3′-forming in eukaryote concerns three elements located in precursor mRNA downstream region: efficiency element (EE), position element (PE) and the actual site for cleavage and polyadenylation. Several base sequences of EE and PE have been proposed by many experiments. The secondary structures of 180 yeast genomic downstream regions (200 bases downstream the stop codon) have been analysed in detail. It is showed that about 86% of EE sites and 89% of PE sites are related to the regions of non-paired loop (hairpin loop, bulge loop, interior loop or multi-branched loop) or to connecting single strand. This result suggests that the identifications and actions of EE and PE by trans-factors, to certain extent, are dependent on the structural features of EE and PE in the secondary structure. According to the secondary structure of mRNA, the prediction accuracy of EE and PE sites may be improved.