© The Author(s) 2018. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. Background. Mycoplasma genitalium can result in pelvic inflammatory disease and adverse pregnancy outcomes. We analyzed data collected from a prospective study of asymptomatic bacterial vaginosis (BV) to determine the natural history of M. genitalium. Methods. Women aged 15–25 years, with asymptomatic BV and ≥2 risk factors for sexually transmitted infection were recruited from 10 sites throughout the United States. Vaginal swab samples were collected at enrollment and through home-based testing every 2 months over 12 months. M. genitalium nucleic acid amplification testing was performed for M. genitalium using transcription-mediated assays (Hologic). The prevalence, incidence, and persistence of M. genitalium, defined as all positive specimens during follow-up, were estimated with 95% confidence intervals (CIs). Adjusted odds ratios (AOR) were calculated using logistic and Poisson regression to evaluate participant characteristics associated with M. genitalium infection. Results. Among 1139 women, 233 were M. genitalium positive, for a prevalence of 20.5% (95% CI, 18.2%–22.9%); 42 of 204 had persistent M. genitalium (20.6%). Among 801 M. genitalium–negative women at baseline, the M. genitalium incidence was 36.6 per 100 person-years (95% CI, 32.4–41.3). Black race (AOR, 1.92; 95% CI, 1.09–3.38), age ≤21 years (1.40; 1.03–1.91), and prior pregnancy (1.36; 1.00–1.85) were associated with prevalent M. genitalium; only black race was associated with incident M. genitalium (P = .03). Conclusions. We identified high rates of prevalent, incident, and persistent M. genitalium infections among young, high-risk women with asymptomatic BV, supporting the need for clinical trials to evaluate the impact of M. genitalium screening on female reproductive health outcomes.