Isoflavonoids and fish oil may be protective against colorectal cancer, but the evidence in relation to breast cancer risk is ambiguous. In the present study, we have investigated the impact of soya-derived isoflavonoids and n-3 fatty acids from fish oil, both individually and in combination, on apoptosis, cell proliferation and oestrogen receptor (ER) expression in the colon and mammary gland of the rat. Female rats were fed diets high in n-3 fatty acids (80 g/kg diet) or soya protein (765 mg/kg diet isoflavones) for 2 weeks, and then killed before the removal of the colon and mammary glands. Cell proliferation and apoptosis were quantified morphologically in whole crypts and terminal end buds. The expressions of ERalpha and ERbeta were measured in colon tissue scrapes and the mammary gland. Fish oil significantly increased apoptosis and decreased mitosis in both tissues, an effect associated with a decrease in the expressions of ERalpha and ERbeta. Soya had no effect on apoptosis in either tissue, but reduced mitosis in the colon (P < 0.001) while increasing it in the mammary gland (P = 0.001). The changes in proliferation were associated with contrasting changes in the ER expression such that fish oil significantly decreased both ERbeta and ERalpha, while soya increased ERalpha and decreased ERbeta. The results may provide a novel mechanism by which n-3 fatty acids could reduce cancer risk, but the interpretation of the results in relation to soya consumption and breast cancer risk requires further investigation.