Introduction Bacterial vaginosis (BV) is a common vaginal condition in women of reproductive age, which has been associated with Chlamydia trachomatis and Neisseria gonorrhoeae among commercial sex workers and women attending sexually transmitted infection clinics. Pathogen-specific associations between BV and other sexually transmitted infections among U.S. military women have not been investigated. Methods A population-based, nested case-control study was conducted of all incident chlamydia and gonorrhea cases reported to the Defense Medical Surveillance System during 2006−2012. Using a density sampling approach, for each chlamydia or gonorrhea case, 10 age-matched (±1 year) controls were randomly selected from those women who were never diagnosed with these infections. Incidence rate ratios were estimated using conditional logistic regression. Statistical analysis was carried out in December 2015. Results A total of 37,149 chlamydia cases and 4,987 gonorrhea cases were identified during the study period. Antecedent BV was associated with an increased risk of subsequent chlamydia (adjusted incidence rate ratio=1.51; 95% CI=1.47, 1.55) and gonorrhea (adjusted incidence rate ratio=2.42; 95% CI=2.27, 2.57) infections. For every one additional episode of BV, the risk of acquiring chlamydia and gonorrhea infections increased by 13% and 26%, respectively. A monotonic dose−response relationship was also noted between antecedent BV and subsequent chlamydia and gonorrhea infection. In addition, an effect modification on the additive scale was found between BV and African-American race for gonorrhea, but not for chlamydia. Conclusions Among U.S. Army women, antecedent BV is associated with an increased risk of subsequent chlamydia and gonorrhea infection.