BACKGROUND Users of the intrauterine device(IUD) may be at increased risk for bacterial vaginosis (BV). Our objective was to compare the incidence of BV in women using the IUD compared to women using combined oral contraceptives (COC), the contraceptive vaginal ring, and the contraceptive patch. METHODS We prospectively recruited women negative for BV at baseline. Monthly, for six months, participants returned a self-obtained vaginal smear for Gram stain by mail. BV was diagnosed by a Nugent score ≥7. We performed Cox proportional hazards regression to investigate associations between demographic and behavioral characteristics, contraceptive method, and incident BV. RESULTS We enrolled 153 women negative for BV at baseline; 90(59%) women who chose the IUD and 63 (41%) who chose COC, ring, or patch. There were 35 women with BV at one or more time points. The incidence of BV was 37.0% among IUD users and 19.3% in COC, ring, and patch users (p=0.03). In the univariate analysis, race, IUD use, intermediate flora, and irregular vaginal bleeding were significantly associated with BV. In the adjusted model, IUD users were no more likely to acquire BV (HRadj 1.28, 95%CI 0.53–3.06)than COC, ring, and patch users. The associations between intermediate flora and irregular bleeding and BV remained significant (HRadj 3.3095% CI 1.51–7.21, and HRadj 2.54, 95% CI 1.03–6.24 respectively). CONCLUSIONS The association between IUD use and BV may be mediated by irregular vaginal bleeding. Intermediate flora is associated with an increased incidence of BV.