Introduction Estrogen receptor (ER)-α and ER-β are believed to mediate the action of estradiol in target tissues [1,2]. These two receptors, which belong to the steroid/retinoic acid/thyroid receptor superfamily [3], contain several structural and functional domains [4] that are encoded by two messenger RNAs that contain eight exons [5,6]. Upon ligand binding, ER-α and ER-β proteins recognize specific estrogen-responsive elements located in DNA in the proximity of target genes, and through interactions with several coactivators modulate the transcription of these genes [7]. Several ER-α and ER-β variant messenger RNAs have been identified in both normal and neoplastic human tissues [8,9,10,11,12]. Most of these variants contain a deletion of one or more exons of the wild-type (WT)-ER messenger RNA. The putative proteins encoded by these variant messenger RNAs would therefore be missing some functional domains of the WT receptors and might interfere with WT ER signaling pathways. Indeed, in vitro functional studies have shown that some recombinant ER-α variant proteins can affect estrogen-regulated gene transcription. For example, the variant protein encoded by exon 3 deleted ER-α variant (ERD3) messenger RNA, which is missing the second zinc finger of the DNA binding domain, has been shown [13] to have a dominant negative activity on WT ER-α receptor action. A similar dominant negative activity has been observed for ERD5 variant protein (encoded by an ER-α variant messenger RNA deleted in exon 5 sequences), which is missing a part of the hormone-binding domain of the WT molecule [14]. Interestingly, a constitutive hormone-independent activity [15] and a WT enhancing activity [16] have also been attributed to ERD5 variant protein in different systems. The relevance of the levels achieved in these transfection experiments to in vivo expression remains unclear. It should also be noted that these functional activities are likely to be cell-type and promoter specific [8]. The discovery that these ER-α variants are expressed in both normal and neoplastic human breast tissues, however, raised the question of their possible role in breast tumorigenesis [8]. We have previously reported an increased relative expression of ERD5 messenger RNA and of ERC4 messenger RNA, another ER-α variant messenger RNA that is truncated of all sequences following the exon 2 of the WT ER-α [17], in breast tumor samples versus independent normal breast tissues [18,19]. In contrast, Erenburg et al [20] recently reported a decreased relative expression of ERD3 messenger RNA in tumor tissues and cancer cell lines versus independent normal reduction mammoplasty samples. Those data, which suggested that alteration in ERD5, ERD3 and clone 4 messenger RNA expression might occur during breast tumorigenesis, were obtained in tissues from different individuals, and possible interindividual differences cannot be excluded. In order to clarify this issue, we investigated the expression of these three variant messenger RNAs in normal breast tissues and their matched adjacent primary breast tumor tissues.