Blood endothelial progenitor cells (EPC) and microparticles (EMP) have been proposed as markers of endothelial dysfunction. The aim of this study was to evaluate a new immunophenotype of EPCs and EMPs in patients with arterial erectile dysfunction (ED) and late-onset hypogonadism (LOH). Fifty patients (58.2 ± 0.7 years) with ED and LOH were enrolled in this study. Their EPC and EMP concentrations were compared with those of 20 patients with arterial ED alone (61.2 ± 1.2 years) and of 20 healthy men (controls; 61.4 ± 1.2 years). EPC (CD45(neg)/CD34(pos)/CD144(pos)) and EMP (CD45(neg)/CD144(pos)/annexin V(pos)) blood concentrations were evaluated by flow cytometry. Patients with ED and LOH or ED alone had significantly higher blood pressure, triglycerides, homeostasis model assessment index of insulin resistance, cavernous artery acceleration time, and intima-media thickness than controls, whereas International Index of Erectile Function score, high-density lipoprotein cholesterol, and cavernous artery peak systolic velocity and resistance index were lower than those of controls. Both EPCs and EMPs were significantly higher in patients with ED and LOH compared with patients with ED alone or controls. Patients with ED alone had EPCs and EMPs significantly higher than controls. In conclusion, patients with ED and LOH showed worse metabolic parameters and cavernous artery parameters, measured by dynamic penile echo color Doppler, and higher EPCs and EMPs compared with patients with ED alone. This suggests that LOH is an additional vascular risk factor and that EPCs and EMPs may be considered predictors of endothelial dysfunction in patients with ED and LOH.