The aim of this study was to investigate the effects of isoflavone-containing soy on circulating sex hormones, biomarkers of bone turnover and lipoprotein profiles. A total of 14 young women received in a randomised crossover design five soy cookies (52 mg isoflavones) or five soy-free cookies (no isoflavones) per day for one menstrual cycle starting 1 week before menstruation. Serum and urine analyses were performed on day 3 after onset of menstruation, 3 days before ovulation, 3 days after ovulation, during the midluteal phase and again 3 days after onset of the next menstruation. With the exception of higher progesterone levels at 3 days before ovulation, soy supplementation did not affect the physiological fluctuations in circulating sex hormones. The ratio of C-telopeptide (a bone resorption marker) to osteocalcin (a bone formation marker) was slightly higher in the midluteal phase of the soy period compared to the control period, indicating an uncoupling of bone resorption and formation processes. Serum levels of total cholesterol, LDL-C and HDL-C were not influenced by soy intake.