We postulated that methoxy-substituted cyclic compounds could inhibit estrogen receptor (ER) negative breast cancer growth in vitro. Therefore, this study assessed the cytotoxic potential of various methoxy-substituted cyclic compounds [7,8-dimethoxyflavone, 4-methoxyphenylacetic acid, 2-methoxyphenylacetic acid, 4-methoxybenzophenone, 5-methoxy-1-indanone, and coenzyme Q0 (CoQ0)] toward ER-negative human breast cancer cells (MDA-MB-231 and SKBr3). Cytotoxicity was assessed using the sulforhodamine B assay. CoQ0 demonstrated the strongest cytotoxicity toward MDA-MB-231 and SKBr3 cells with IC50 values of 1.7 μmol/l and 3.1 μmol/l, respectively, whereas the other compounds were either much less potent or completely lacked cytotoxicity toward both breast cancer cell lines. Therefore, only CoQ0 was examined for its ability to modulate cell cycle progression and induce apoptosis. Cell cycle experiments, using propidium iodide staining and flow cytometry, demonstrated that CoQ0 at 7.5 μmol/l increased the proportion of MDA-MB-231 cells in G1/G0-phase by 16.6±0.6% of control (P<0.05), and increased in the proportion of S-phase SKBr3 cells by 37.8±5.8% over control (P<0.05). Induction of apoptosis was determined using propidium iodide/Annexin-V-FLUOS staining followed by flow cytometry. The results demonstrated that treatment with CoQ0 (7.5 μmol/l) increased the proportion of apoptotic MDA-MB-231 and SKBr3 cells by 12-fold and 4-fold over control (P<0.05), respectively. Thus, CoQ0 is a potent cytotoxic drug that induces apoptosis and modulates cell cycle progression in ER-negative breast cancer cells. Therefore, CoQ0 is an appropriate candidate for further study and development as a potential drug for ER-negative breast cancer.