The presence of estrogen receptor alpha (ERalpha) is the basis for treating breast cancer patients with targeted molecular therapies that block estrogen stimulation of breast cancer cell division. Currently, the ERalpha presence is determined by microscopically scoring the slides subjected to immunohistochemistry. This method is not quantitative, cannot distinguish between all the known ERalpha isoforms, and requires large amounts of tumor tissue. We describe here a real-time PCR-based molecular approach that can be applied to determine mRNA copies of eight ERalpha isoforms in picogram amounts of total RNA from clinical samples. Each isoform mRNA is quantified using a specific primer pair and a 5'FAM- and 3'TAMARA-labeled probe in comparison with a standard curve constructed with known copy numbers of its respective reverse-transcribed cRNA. Seven alternatively spliced isoforms were quantified using splice-targeted primers. The cRNAs for eight isoforms were generated by in vitro transcription of their respective coding sequences. The sensitivity of detection with reverse-transcribed cRNAs is as low as 100 copies. The devised assays can detect ERalpha cDNAs reverse transcribed from as low as 50-100 pg of total RNA from breast cancer tissues. The applicability of the devised assays for profiling eight ERalpha isoform mRNAs is demonstrated using 6 breast cancer cell lines and 10 breast cancer tissues. It is expected that these assays could be applied to profile ERalpha isoforms in any estrogen-responsive tissues. In addition, these methods could highly facilitate the design of tissue-specific selective estrogen receptor modulators to treat breast cancers and other estrogen-related abnormalities.