Soy isoflavones supplements, which are phyto-oestrogens widely used as alternatives to alleviate menopausal syndromes or prevent chronic diseases, may exert oestrogenic and anti-oestrogenic activities. This study aimed to investigate the effects of soy isoflavones supplement on oestrogen-related autoimmune disease, such as systemic lupus erythematosus, using autoimmune-prone female MRL-lpr/lpr mice. Eighty mice of 8 weeks were divided into five groups: 0 (Control), 2 (Isf 2), 10 (Isf 10) and 20 (Isf 20) mg/kg BW/day Phyto Soya isoflavones or 0.375 mg/kg BW/day tamoxifen (TAM) as the positive control, by tube-feeding. Some mice were killed at age 15 weeks for cellular cytokine secretion. The data suggested that the Isf 20 and TAM groups had higher weight gain and survival compared with the control group. At age 22 weeks, the Isf 20 group still had 75% survival comparable to mice treated with TAM. At age 14 weeks, the TAM group showed significantly lower serum anti-double-stranded (ds) DNA IgG and anti-cardiolipin IgG. The mice in the Isf 10 and Isf 20 groups also had lower anti-dsDNA IgG and anti-cardiolipin IgG. The interferon (IFN)-gamma secretion from mitogen-stimulated T cells in the Isf 20 and TAM groups were significantly lower than those of control mice. Furthermore, the oestrogenic activity of the methanol extracts of soy isoflavones for oestrogen receptor (ER)beta, but not ERalpha, significantly increased, suggesting that soy isoflavones have a selective modulation of ER activation. Thus, soy isoflavone supplementation did not aggravate murine lupus, but apparently ameliorated the disease.