Mycoplasma genitalium (MG) is a common cause of nongonococcal cervicitis and urethritis. We investigated the demographic and clinical characteristics of patients tested in Denmark with the Conformité Européenne (CE)/in vitro diagnostics (IVD) Aptima Mycoplasma genitalium assay (CE/IVD AMG; Hologic) and examined the clinical significance of the higher sensitivity of the TMA-based MG assays. From March to June 2016, urogenital and extragenital specimens from consecutive attendees at a sexually transmitted infection clinic in Copenhagen, Denmark were tested with the CE/IVD AMG assay (TMA-based), the research-use-only MG Alt TMA-1 assay (Hologic), a laboratory-developed TaqMan mgpB quantitative real-time PCR (qPCR), and the Aptima Combo 2 (CT/NG; Hologic). Demographic characteristics and clinical symptoms were collected from the patient records. There were 1,245 patients included in the study. The MG prevalence among female subjects was 9.4%, and the MG prevalence among male subjects was 8.7%. Compared to the TMA-based assays, the sensitivity of the PCR-based MG assay was 64.52%, and 55 specimens from 48 individuals were missed in the mgpB qPCR. Of these, 26 individuals (54.2%) were symptomatic, whereas, among 64 individuals with concordant results, 30 individuals (46.9%) were symptomatic; no statistically significant difference was found between the groups (P = 0.567). The improved sensitivity of the TMA-based assays resulted in diagnoses of more patients with clinically relevant symptoms for which antibiotic treatment is indicated. However, approximately half of the MG-infected patients reported no symptoms, and future research is needed to investigate the pros and cons of diagnosing and treating MG in asymptomatic subjects.