Background Women with vaginal microbial community state types (CST) with high diversity and a paucity of Lactobacillus crispatus have increased risk of HIV acquisition. Identifying host genetic factors associated with the vaginal microbial composition may aid in elucidating the biological mechanisms regulating these microbial traits and inter-individual variations in associated diseases. Methods We conducted genome-wide associations studies (GWASs) on vaginal microbiome traits on 171 Kenyan women. Study participants were genotyped using the Infinium Global Screening Array and 16S rRNA gene amplicon sequencing was performed to characterize the vaginal microbiome. Linear and logistic regression were performed, adjusting for age and principal components of genetic ancestry, to evaluate the association between L. crispatus, L. iners, G. vaginalis, Shannon diversity index, and CST with host genetic single nucleotide polymorphisms (SNPs). Pathway enrichment analyses were performed to identify biological processes putatively associated with the vaginal microbiome traits. Results At baseline, the median age of study participants was 22 years (IQR: 22 – 25) with 22% having Bacterial vaginosis (Nugent score 7-10). L. crispatus and L. iners were present in 24% and 83% of samples with a mean relative abundance of 31% and 45%, respectively. The most significant SNPs associated were: rs73330467 located between LOC101927488-GRAMD2B ( P =4.79x10 -6 ) for L. crispatus ; rs527430 in the FOXD2-TRABD2B ( P =6.98x10 -7 ) region for L. iners ; rs1229660 in the SNX10-LOC441204 ( P =4.65x10 -6 ) region for G. vaginalis; rs972741 in the ZKSCAN2-HS3ST4 ( P =8.52x10 -7 ) region for Shannon diversity index; and rs2302902 in ELK3 ( P =3.09x10 -6 ) for CST. During pathway enrichment analysis, Toll-like receptors, cytokine production, and other components of innate immune response were associated with L. crispatus, L. iners, and CST. Multiple genomic loci were replicated, including IL-8 (Shannon, CST), TIRAP ( L. iners , Shannon), TLR2 (Shannon, CST), MBL2 ( L. iners , G. vaginalis , CST), and MYD88 ( L. iners, Shannon). Conclusions We identified numerous genetic loci on several pathways related to host immunity and infection that were associated with vaginal microbiome traits, providing insight into potential host genetic influences on vaginal microbiome composition. This new information should guide larger longitudinal studies, with genetic and functional comparison across microbiome sites within individuals, and across populations.