Dysregulation of total estrogen receptor beta (ERbeta) expression has been implicated in breast tumorigenesis. The ERbeta gene yields five exon 8 alternatively spliced transcripts (ERbeta1-5), which encode proteins with different C-terminal amino acids. Individual expression analysis of these transcripts may provide new insights into estrogen signaling in breast cancer. We measured mRNA levels of total ERbeta and its five isoforms in normal tissues, breast carcinomas from post-menopausal patients, and breast cancer cell lines by means of real-time reverse transcription-polymerase chain reaction and fluorescent fragment analysis. In various normal human tissues, ERbeta1-5 isoforms displayed different qualitative and quantitative expression patterns that were consistent with previous reports. Total ERbeta mRNA levels were significantly lower in breast tumors than in normal breast tissues (38-fold lower, P < 0.001), mainly due to lower expression of ERbeta1 and ERbeta2 (ERbeta5 expression was similar in the two tissue types). This altered expression pattern of ERbeta isoforms in breast cancer should be taken into account in future ERbeta-based clinical applications.