Based on the hypothesis that isoflavones are absorbed more efficiently from fermented than from non-fermented soya foods, we compared the urinary isoflavonoid excretion (UIE) after intake of miso soup or soya milk. We recruited twenty-one women with Japanese ancestry who consumed standardized soya portions containing 48 mg isoflavones. On day 1, half the women consumed soya milk, the other half started with miso soup. On day 3, the subjects ate the other soya food and on day 5, they repeated the first food. Each participant collected a spot urine sample before and an overnight urine sample after soya food intake. All urine samples were analysed for daidzein, genistein and equol using LC-MS and were expressed as nmol/mg creatinine. We applied mixed models to evaluate the difference in UIE by food while including the baseline values and covariates. Relative to baseline, both groups experienced significantly higher UIE after consuming any of the soya foods. We observed no significant difference in UIE when soya milk was compared to miso soup (P = 0.87) among all women or in the seven equol producers (P = 0.88). Repeated intake of the same food on different days showed high reproducibility within subjects. These preliminary results indicate similar UIE after consuming a fermented soya food (miso) as compared to a non-fermented soya food (soya milk). Therefore, recommendations favouring fermented soya foods are not justified as long as the intestinal microflora is capable of hydrolysing the isoflavone glucosides from non-fermented soya foods.