To investigate whether estrogen receptor abnormalities are associated with resistance of breast cancer to endocrine therapy, we compared estrogen receptor mRNA between normal breast tissue and carcinoma. Using the RT-PCR, paired cancer and normal breast tissue specimens from 15 patients were analyzed. Exon-deleted variants were found in both tumor and normal tissue, with differences of variant expression between normal and tumor tissue being observed. One patient showed multiple deletions in the hormone-binding domain. Alterations in the amount and/or kind of variant ER expression may be important in determining the response of breast cancer to endocrine therapy.