Underlying endothelial dysfunction (EnD) may present in the early stage of ED or psychogenic ED. We retrospectively evaluated 191 ED patients with effective nocturnal penile tumescence and rigidity (NPTR) recording, including detailed medical and psychosexual history, International Index of Erectile Function-5 and vascular parameter. All patients were allocated into psychogenic and organic groups according to the NPTR test. Brachial artery flow-mediated dilation (FMD) was used to diagnose EnD, and ED patients were classified into two groups: non-EnD (FMD10) and EnD (FMD0.05). In conclusion, NPTR cannot effectively identify the underlying vasculogenic ED from psychogenic ED. Psychogenic causes may cause or aggravate EnD in these ED patients with normal NPTR.