Background: Untreated urogenital Chlamydia trachomatis spontaneously clears from the female reproductive tract in 16-44% of cases, but the host mechanisms supporting clearance are undefined. Vaginal microbiota may support clearance through effects on immune responses, and epithelial cell and chlamydia proliferation. We determined the association between bacterial vaginosis (BV) and chlamydia persistence versus spontaneous clearance within twelve-week intervals. Methods: The NIH Longitudinal Study of Vaginal Flora followed 3,620 reproductive-age women every three months for one year (1999-2002). Screening for chlamydia in asymptomatic participants at baseline was initiated after ligase chain reaction became available. Endocervical samples which were not immediately screened were tested for chlamydia after study completion. Chlamydia clearance and persistence were evaluated between consecutive visits without chlamydia-active antibiotic use (N=432 participants, N=632 chlamydia cases). Associations between Nugent score (0-3, no BV; 4-10, intermediate/BV), Amsel-BV, and subsequent chlamydia persistence versus clearance at the next visit were modeled with alternating logistic regression models. Among a subgroup of 68 participants experiencing both chlamydia clearance and persistence during their one-year follow-up, we assessed participants as their own controls using conditional logistic regression. Results: Spontaneous clearance occurred within the next 12 weeks for 49% of chlamydia cases (311/632). Compared to participants without BV, chlamydia cases with intermediate/BV scores had higher odds of chlamydia persistence versus clearance at the next visit adjusting for age, contraception, condom use, and marital status (aOR: 1.84, 95% CI: 1.27-2.69). Adjusting for BV symptoms did not affect results. Findings were similar for Amsel-BV (aOR: 1.37, 95% CI: 0.97-1.93). Nugent-BV scores (7-10) remained associated with persistence after excluding prevalent chlamydia at baseline (aOR: 1.84, 95% CI: 1.04-3.25), and after censoring participants following their first event (aOR: 1.82, 95% CI: 1.10-2.98). Intermediate/BV scores were associated with 3-fold higher odds of chlamydia persistence (95% CI: 1.11-9.99) among participants contributing both persistence and clearance events. Conclusion: BV was associated with a greater odds of chlamydia persistence, while those without BV were more likely to spontaneously resolve their chlamydia infection without treatment. Novel interventions to prevent chlamydia infection and subsequent reproductive sequelae, and promote clearance may include optimizing the vaginal microbiota.