A novel estrogen receptor mRNA splice variant which lacks the entire exon 5 and part of exon 4 and 6 was identified using reverse transcription PCR in human breast carcinomas. The variant was translated in vitro and produced a protein of approximately Mr 31000 which lacked the ligand binding domain. The binding of the variant estrogen receptor (ER) to a synthetic estrogen-responsive element (ERE) was compared with that of the wild-type ER (wtER). The variant ER bound weakly to the synthetic ERE, both in the presence and absence of estradiol, whilst the wtER bound strongly in the absence and the presence of estradiol. When wtER and variant ER were simultaneously translated in vitro, no heterodimerization was observed using band shift assay. Addition of increasing amounts of variant ER protein to the wtER in the ERE binding reaction showed that the variant protein competed with the binding of the wtER to the synthetic ERE. Furthermore, variant ER are not transcriptionally active. The variant was also expressed in 96% of the 102 breast tumours analysed, of which 62 were tamoxifen-resistant tumours. The expression of this variant was significantly higher (relative to ER) in untreated ER-positive breast tumours which were both progesterone receptor (PgR) negative and pS2 negative phenotype.