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Introduction Bacterial vaginosis (BV), characterized by Lactobacillus depletion and replacement by facultative or anaerobic bacteria, impacts up to 30% of women and associates with negative reproductive health outcomes. We used a systems immunology approach to investigate cellular and molecular inflammation associated with BV. Methods Matched cervical cytobrush and cervicovaginal lavage were collected from BV− (n=16) and BV+ (n=11) women. Cytobrushes were immunophenotyped by flow cytometry and lavages were analyzed by tandem mass spectrometry. Differences in immune cell levels were evaluated with Mann-Whitney U tests, and assessed against host and bacterial proteins using Spearman’s Rank correlations. Results There were no clinical or demographic differences between BV+ and BV− women, including age (range 22–49), birth control use and STI history. Proteomic analysis identified 1085 human proteins and 516 bacterial proteins from 14 genera, including Lactobacillus, Gardnerella, and Mobiluncus. Long living neutrophils (CD49d+) were significantly increased in BV+ women (p=0.0005), and associated with cell adhesion (p=4.04E-5), T cell mediated immunity (p=0.004), and regulation of myeloid differentiation (p=8.63E-16) pathways. CD49+ neutrophils correlated positively with Mobiluncus (p=0.040, R2=0.49) and negatively with Lactobacillus (p=0.035, R2=−0.498). Discussion This data indicates that cervical neutrophil survival is increased in women with BV. These cells associated with anaerobic bacteria and molecular pathways of immune activation. Studies are ongoing to delineate the relationship between BV-associated bacteria and neutrophil functionality, which may have implications for BV treatment.