Adjuvant tamoxifen therapy is effective in reducing the risk of recurrence and death in patients with estrogen-receptor-positive breast cancer. However, the development of acquired resistance to tamoxifen limits its clinical effectiveness. To determine the effects of tamoxifen on breast cancer cells, long-term cultures of the breast cancer MCF-7 cell line, treated with tamoxifen, were established. Gene expression profiles of tamoxifen-treated and untreated MCF-7 cells were characterized using the Clontech Atlas human cancer 1.2 array, representing 1,176 genes. RNA was extracted from tamoxifen-sensitive cells 4 days and 6 weeks after commencement of treatment with tamoxifen, as well as from untreated MCF-7 cells at the same time points. Only gene expression differences greater than twofold were considered. At 4 days, 13 genes were found to be overexpressed and 2 genes were underexpressed in the tamoxifen-treated MCF-7 cells compared with the untreated MCF-7 cells. In the tamoxifen-treated MCF-7 cells harvested at 6 weeks, 16 genes were overexpressed and 5 genes were underexpressed compared with the treated cells harvested at 4 days. Wnt-5a, disheveled homologue 1, cyclin kinase inhibitor p19INK4D and the signaling lymphocytic activation molecule were overexpressed in both of the comparisons. Gene expression profiling is useful for the rapid identification of genes differentially expressed during tamoxifen treatment.