In eleven patients with metabolic syndrome in the initial stage, the reduction of arteriosclerotic nanoplaque formation amounted to 14.3 2.9% (p < 0.0077) and of nanoplaque size to 23.4 3.7% (p < 0.0004), respectively, after 2-months of treatment with Ginkgo biloba extract. Additionally, superoxide dismutase (SOD) and glutathione peroxidase (GPx) activities were upregulated by 19.6 10.0% (p < 0.0785) and 11.6 2.3% (p < 0.001), respectively, the quotient oxLDL/LDL lowered by 21.0 4.3% (p < 0.002), and lipoprotein(a) concentration decreased by 26.3 4.8% (p < 0.001) in the patients' blood. The concentration of cAMP and cGMP was augmented by 43.5 12.0% (p < 0.001) and 32.9 10.4% (p < 0.001), respectively. Surprisingly, we found a lowering of the serum Ca²⁺ concentration by 5.4 1.6% (p < 0.0076) from 2.37 0.03 to 2.24 0.04 mmol/L (p < 0.0069). Apart from an additional vasodilatory effect, the lowered extracellular Ca²⁺ concentration affects nanoplaque formation restrictively, since this is a Ca²⁺ driven process. Furthermore, we could show a favourable development of the biomarkers 8-iso-PGF_2a, oxLDL/LDL, SOD, GPx (oxidative stress), hs-CRP, MPO, TNFa, TGFb₁ (inflammatory status) and MMP-9 (plaque stability). The markers selected here are suited to provide a comprehensive risk profile for the prevention of arteriosclerosis.