Experiments were undertaken to characterize mRNAs coding for the estrogen receptor (ER) in the human breast cancer cell line T47D. We report here the isolation of cDNAs corresponding to three isoforms of this receptor in addition to a majority of wild-type clones. Sequence analysis showed that these isoforms are generated through alternative splicing. None of the alternatively spliced isoforms of ER is able to bind to an estrogen-responsive element (ERE) in a gel mobility shift assay in vitro or to activate transcription of a reporter gene containing an ERE in vivo. One isoform, ER delta E3, which harbors a deletion of exon 3 encoding the second zinc finger of the DNA-binding domain, inhibits estrogen-dependent transcription activation in a dominant negative fashion when it is cotransfected with the wild-type ER and reporter plasmid. It also inhibits DNA binding of wild-type ER in a gel mobility shift assay in vitro. Since ER delta E3 is not able to bind to its response element, the observed inhibitory effect probably occurs through protein-protein interactions. This could involve the formation of a heterodimer between mutant and wild-type receptors, competition for a limiting transcription factor, or both. These results may have implications for understanding the loss of estrogen responsiveness that frequently occurs in breast cancer.