Background: Clinical trials have suggested that the gut microbiome can modulate immunotherapy outcomes with checkpoint inhibitors (Kroemer et al, Nat rev immunology. Jan 2018). However, the role of cervical microbiome has not been investigated. We studied the effect of cervical microbiome on outcomes of a novel therapeutic HPV vaccine in women with high grade cervical neoplasia. Methods: We collected 65 cervical samples (34 pre-screen and 31 post-vaccination) from 34 women enrolled in a phase 1 therapeutic vaccine trial (Coleman et al. Cancer Immunol Immunotherapy. May 2016). Whole DNA was isolated from cervical Thinprep samples using the Qiagen DNA Mini Kit and amplified by PCR using a bacterial 16sRNA gene primer. eOTUs were identified using V1-V9 16S rRNA gene hybridization with G4 Phylochip™ (Second Genome, South San Francisco, CA). Alpha and beta diversity metrics were calculated. We used PERMANOVA analysis to test for associations of phylogenetic composition with patient demographics; HPV status; HLA type; circulating Th1, Th2, and Treg cells; local TFoxp3 cells and clinical response to the vaccine. Responders and non-responders were defined based on histological regression of cervical lesions. Results: Richness ranged from 72 to 365 eOTUs per sample, and Prevotellaceae and Lactobacillaceae were the most abundant families observed. We found that pre-screen samples from vaccine non-responders, as compared to responders, were enriched with the phyla Caldithrix, Nitrospirae and family Mycoplasmataceae and an unclassified family from order Entomoplasmatales. HPV16 status and HLA B40 status were significantly associated with beta diversity. Measures of pre- and post-vaccination alpha and beta diversity were not statistically significantly associated with response to vaccine. Also, we observed no correlations of microbiome metrics with immune parameters. Conclusions: Study findings suggest that cervical microbial composition may predict non-responsiveness to a therapeutic vaccine given to treat high-grade cervical neoplasia. Observed associations of cervical microbial composition with HLA B40 and HPV 16 status are of interest but require further investigation. Clinical trial information: NCT01653249