BACKGROUND: Inflammatory markers and insulin resistance are independent cardiovascular risk factors and are thought to be influenced by sex steroids. We investigated changes of inflammatory markers and estimates of insulin resistance during the menstrual cycle, their variances, and their relationship to each other, sex steroids, and regional body fat distribution. METHODS: Eight normal weight (body mass index, 21.6 +/- 1.9 kg/m(2)) and nine overweight (body mass index, 30 +/- 2.4 kg/m(2)) young women with normal ovarian function were assessed 15 times throughout the menstrual cycle. Regional fat distribution was assessed using dual x-ray absorptiometry. RESULTS: Concentrations of highly sensitive C-reactive protein (hs-CRP) changed significantly during the menstrual cycle and were highest in the early follicular phase (P < 0.00001). SHBG concentrations were stable in the follicular phase but increased in the luteal phase (P < 0.00001). During the follicular phase, estimates of insulin resistance had a higher within-subject variance when determined by the homeostasis model assessment index (42%) than when estimated by SHBG concentrations (5%, P < 0.05). During the menstrual cycle, using repeated measurements, hs-CRP correlated inversely to estradiol (beta-coefficient, -0.23, P < 0.0001) and SHBG concentrations (beta-coefficient, -0.83, P = 0.004). Central accumulation of body fat correlated to the mean hs-CRP concentration (r = 0.63, P = 0.007) and the mean homeostasis model assessment index for insulin resistance (r = 0.75, P = 0.001). CONCLUSION: We demonstrate that serum concentrations of hs-CRP and SHBG significantly change during the menstrual cycle. We reveal a close link between sex steroids, subclinical inflammation, insulin resistance, and body fat distribution in regularly menstruating women.