ABSTRACT. The microbial community of the reproductive apparatus, when known, can provide information about the health of the host. Metagenomics has been used to characterize and obtain genetic information about microbial communities in various environments and can relate certain diseases with changes in this community composition. In this study, samples of vaginal surface mucosal secretions were collected from five healthy cows and five cows that showed symptoms of reproductive disorders. Following high-throughput sequencing of the isolated microbial DNA, data were processed using the Mothur software to remove low-quality sequences and chimeras, and released to the Ribosomal Database Project for classification of operational taxonomic units (OTUs). Local BLASTn was performed and results were 6519 Vaginal microbiota diversity of healthy and diseased cattle ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (2): 6518-6528 (2015) loaded into the MEGAN program for viewing profiles and taxonomic microbial attributes. The control profile comprised a total of 15 taxa, with Bacteroides, Enterobacteriaceae, and Victivallis comprising the highest representation of OTUs; the reproductive disorder-positive profile comprised 68 taxa, with Bacteroides, Enterobacteriaceae, Histophilus, Victivallis, Alistipes, and Coriobacteriaceae being the taxa with the most OTU representation. A change was observed in both the community composition as well as in the microbial attributes of the profiles, suggesting that a relationship might exist between the pathogen and representative taxa, reflecting the production of metabolites to disease progression.