Metallothioneins (MTs), a group of ubiquitous metalloproteins, comprise isoforms encoded by ten functional genes in humans. Different MT isoforms possibly play different functional roles during development or under various physiological conditions. The MT-1E isoform mRNA has been recently shown to be differentially expressed in oestrogen receptor (OR)-positive and OR-negative breast cancer cell lines. In this study, we evaluated MT-1E mRNA expression via semi-quantitative RT-PCR in 51 primary invasive ductal breast cancer tissues, concurrently with OR-positive and progesterone receptor (PR)-positive MCF7 cells, OR-negative and PR-negative MDA-MB-231 cells and PR-transfected MDA-MB-231 breast cancer cells (ABC28). We demonstrated significantly higher MT-1E mRNA expression in OR-negative compared with OR-positive breast cancer tissues (P = 0.026). MCF7 cells lacked MT-1E mRNA expression, while both OR- and PR-negative MDA-MD-231 cells exhibited a high level of MT-1E mRNA expression. The level of MT-1E mRNA expression in progesterone-treated and -untreated ABC28 cells remained similar as the parental cell line MDA-MB-231-C2 cells. The results suggest that MT-1E may have specific and functional roles in OR-negative invasive ductal breast cancers, possibly mediated via effector genes downstream of the oestrogen receptor, but not through the PR pathway.