Goals: In the EU‐funded FP7 project BIOCLAIMS extensive metabolic phenotyping of healthy subjects is performed to identify and characterize biomarkers of metabolic robustness. This study aims at elucidating changes in these biomarkers during the menstrual cycle.Subjects & methods: Healthy women (n=26) not taking hormonal contraceptives, aged 34±6.1 y, were investigated after an overnight fast at early (day 5.9±0.97, t1) and late follicular phase (day 12.0±1.82, t2), and mid (day 19.6±2.52, t3) and late luteal phase (day 25.2±2.12, t4). Time points of investigation were scheduled based on basal body temperature records prior to the study. Phenotyping included body composition (bioelectrical impedance), endothelial function (flow‐mediated dilatation, FMD), activation of p65, p50 and cRel subunits of transcription factor nuclear factor κB (NF‐κB) in peripheral blood mononuclear cells (TransAM®), vitamin A, C, E, carotenoids, symmetrical (SDMA), asymmetrical dimethyl (ADMA) and homo‐arginine (HA) and human mercaptalbumin (HMA), all by HPLC, leptin, adiponectin by ELISA; lipid status; vitamin B12 and folic acid by clinical chemistry.Results: Significant differences between time points were observed for NF‐κB p65 activation (P=0.017), plasma ascorbate (P<0.001), B12 (P=0.002), folic acid (P=0.032), ADMA (P<0.001), SDMA (P=0.037), and HA (P=0.012), and LDL cholesterol concentrations (P<0.001), all significant for t1>t3, while FMD (P=0.011), leptin (P=0.024) and adiponectin (P=0.027) were significant for t3>t1. There were no significant changes in HMA, body composition and other variables.Conclusions: Follicular and luteal phase differentially affect the metabolic phenotype of healthy women. Changes between t1 and t3 can be explained by previously shown estrogen effects, including reduction of NF‐κB activation in primary human macrophages, enhanced leptin synthesis and improvement of FMD due to decreases in ADMA, a nitric oxide synthase inhibitor.Grant Funding Source: Supported by European Commission, FP7, contract 244995, and Austrian Government (bmwf)