In order to analyze the structures of the 5′-untranslated region of estrogen receptor alpha (ERα) mRNA in human uterine endometrium (Em), total RNA from Em was analyzed by 5′-rapid amplification of the cDNA ends method with antisense primer located on exon 1 of human ERα gene. Three isoforms of 5′-RACE clones were obtained: ERα mRNAs containing exon (A) (the upstream region of exon 1), exon C, and exons F-E2 (we adopted the nomenclature of 5′-untranslated exons of the Gannon group). The results imply that the major isoforms of ERα mRNA expressed in Em are these three isoforms. Moreover, reverse transcription-polymerase chain reaction (RT-PCR) analysis was carried out on Em, ovary (Ov) and liver (Li) mRNAs to detect the novel isoforms of ERα mRNA in these tissues, using sense primers located on exons (A), B, C, F, and E1, and antisense primer located on exon 1. As a result, in addition to the previously reported ERα mRNA isoforms containing exons (A), B, C, F-E2 and E1-E2 on exon 1, we identified two novel isoform mRNAs in which exons F and E1 were directly spliced onto exon 1. Differential distributions of these isoforms of ERα mRNAs in Em, Ov and Li were demonstrated by RT-PCR-Southern blot analysis. These results, together with the previous reports by others, indicate that there are at least ten isoforms of ERα mRNA containing different 5′-untranslated regions, exons (A), B, C, D, T1-T2, T1, F-E2, F, E1-E2 and E1, expressed in human, and that these are involved in tissue specific expression of the gene.