BACKGROUND: Several variant estrogen receptor (ER) mRNAs are present in various cell lines of human breast cancer, and are considered to be one reason for the loss of hormone dependence. The purpose of this study was to assess the ER variants in human various breast tissues, and to investigate the correlation between the expression of ER variants and ER/progesterone receptor (PgR) status. METHODS: The frequencies of 3 ER splice variants (del 2/3, del 5, and del 7) were assessed in 24 benign and 76 malignant breast lesions by the reverse transcription ]polymerase chain reaction (RT-PCR) method and compared with histopathological features. ER and PgR proteins were analyzed using enzyme immunoassay (EIA) and immunohistochemical assay (IHA) in 68 cases of cancer to determine whether aberrant variants influence the status of either protein. RESULTS: Deletions of exons 5 and 7 (del 5 and 7) were more frequent than the deletion of exon 2/3 (del 2/3) in both benign and malignant lesions, and the expression of del 5 and del 7 seemed to correlate with epithelial overgrowth. There was no significant difference between the ER/PgR protein status and the expression of each ER variant in breast cancer. CONCLUSION: The expression of ER splice variants is not uncommon in human breast diseases. The abnormal ER structures in this study are not a main factor for tamoxifen insensitivity or an important regulators of PgR expression.