Sex steroid hormone progesterone is known to have profound effects on the growth and differentiation of the normal mammary gland and malignant breast epithelial cells. In vitro progesterone and synthetic progesterone-like compounds (progestins) inhibit breast cancer cell growth. Medroxyprogesterone acetate (MPA) is a synthetic hormone widely used in the adjuvant treatment of advanced breast cancer, hormone replacement therapy and in oral contraceptives. It is a paradoxical hormone, since it inhibits breast cancer cell proliferation, but has also been implicated in increased breast cancer risk. To better understand the molecular mechanism by which cell proliferation and differentiation are regulated by progesterone and MPA in human breast cancer, we utilized cDNA microarray and quantitative real-time RT-PCR methods to identify their target genes. This study describes novel progestin/progesterone target genes in breast cancer cells and, notably, novel target genes that elucidate the underlying molecular mechanism of the dual role progestins play in the breast. A cDNA microarray containing 3000 genes showed notable regulation in 30 and 27 genes by MPA and progesterone, respectively. Only 6 out of the 30 genes regulated by MPA are down-regulated, but no progesterone down-regulation was observed. Overlapping in gene regulation by progesterone and MPA occurred, but the majority of genes regulated by these hormones were distinct. Given that progestins both stimulate and inhibit cancer cell growth, we report our findings on novel progestin and progesterone targets, which could explain the paradoxical actions of progestins in the breast.