Almost all physicians involved in treating sexually transmitted infections recognize the specific clinical manifestations of patients with urethritis. However, in previous studies, the diagnosis of gonococcal urethritis was based on cultures or staining methods. In this study, we examined in detail the clinical manifestations of patients with urethritis diagnosed by the nucleic acid amplification test (NAAT). A total of 154 patients with male urethritis were included in the study. The NAAT could distinguish 64 patients with gonococcal urethritis, 45 patients with chlamydial urethritis, and 45 patients with nongonococcal and nonchlamydial urethritis. Forty-three (67.2%) patients with gonococcal urethritis had more severe symptoms, i.e., moderate or profuse urethral discharge, and cloudy or purulent discharge, than patients with chlamydial urethritis, nongonococcal and nonchlamydial urethritis. There were 39 (86.7%) patients in the chlamydial urethritis group with mild symptoms, clear discharge or none, and moderate or profuse discharge. Although the diagnosis of male urethritis can be performed by microbiological examination, the typical symptoms help us to distinguish each type of urethritis and understand this kind of disease.