To establish a model of endocrine resistant breast cancer that is associated with loss of estrogen receptor (ER), MCF7 cells were transfected with several plasmid constructs intended to produce intracellular double stranded hairpin RNA to be processed into siRNA directed against different regions of the ERalpha mRNA. Stably transformed cells were propagated in long-term culture. One of these lines, designated pII, was selected for further analysis. pII cells exhibited reduced levels of ERalpha mRNA and protein as well as several estrogen-regulated genes assessed by real-time PCR and were unresponsive to addition of estradiol and tamoxifen. Higher levels of ERbeta were measurable as compared with parental MCF7 cells. There was an unexpected decrease in expression in members of the EGFR family in contrast with observations reported for ER-negative tumours or some other established endocrine-independent lines. Microarray gene analysis comparing expression in parental MCF7 with pII cells in both serum-synchronised and non-synchronised conditions highlighted a spectrum of other genes that were expressed at different levels compared to the parental MCF7 cells. Genes showing the greatest change were mostly common between synchronized and unsynchronised cells; GRB7, PSMD7, KRT19, KRT18, AKT1, SYNCRIP, CYB5A and EVL for down-regulated in pII and QDPR, VIM, CD68, CA9, STMN1, CDK2, CTSC for up-regulated in pII cells. Notably, the decreased expression of epithelial keratins 18 and 19 and an increase in vimentin and in a macrophage marker CD68, is suggestive of an epithelial to mesothelial transition. Further characterisation of these cells particularly with respect to the factors controlling their growth may contribute to a better understanding of the behaviour of cells that have become endocrine independent by loss of ER function.