The vaginal microbiota is known to impact women's health, but the biological factors that influence the composition of the microbiota are not fully understood. We previously observed that levels of glycogen in the lumen of the vagina were higher in women that had a high body mass index (BMI). Vaginal glycogen is thought to impact the composition of the vaginal microbiota. We therefore sought to determine if BMI was associated having or not having bacterial vaginosis (BV), as determined by the Amsel criteria. We also hypothesized that increased blood glucose levels could lead to the previously-observed higher vaginal glycogen levels and therefore investigated if hemoglobin A1c levels were associated with BV. We analyzed data from the Women's Interagency HIV Study using multiple multivariable (GEE) logistic regression models to assess the relationship between BMI, BV and blood glucose. Women with a BMI >30 kg/m2 (obese) had a lower rate (multivariable adjusted OR 0.87 (0.79-0.97), p = 0.009) of BV compared to the reference group (BMI 18.5-24.9 kg/m2). There was a significantly lower rate of BV in post-menopausal obese women compared to the post-menopausal reference group, but not in pre-menopausal women. HIV- post-menopausal obese women had a significantly lower rate of BV, but this was not seen in HIV+ post-menopausal obese women. Pre-menopausal women with a higher hemoglobin A1c (≥6.5%) had a significantly lower rate (multivariable adjusted OR 0.66 (0.49-0.91), p = 0.010) of BV compared to pre-menopausal women with normal hemoglobin A1c levels (<5.7%), but there was no difference in post-menopausal women. This study shows an inverse association of BMI with BV in post-menopausal women and hemoglobin A1c with BV in pre-menopausal women. Further studies are needed to confirm these relationships in other cohorts across different reproductive stages and to identify underlying mechanisms for these observed associations.