Since other viruses can influence expression of human papillomavirus (HPV) 16 E6-E7 genes in vitro, this study addressed whether specific vaginal bacteria do so as well. The vaginal microflora of 18 women with cervical intraepithelial neoplasia (CIN) or normal histology and HPV 16 infection, was evaluated by quantitative culture. Expression of HPV 16 E6-E7 oncogenes was assessed in exfoliated cervical cells by quantitative polymerase chain reaction. HPV 16 expression was also quantitated in CaSki carcinoma cell line cocultured with Bacteroides fragilis or Lactobacillus acidophilus. Isolation of Lactobacillus sp. (p = 0.05) and expression of the E6*II transcript (p = 0.03) were associated with low-grade CIN or normal histology. However, changes in E6-E7 expression were not associated independently with isolation of a specific microorganism. Similarly, expression of HPV 16 E6-E7 oncogenes in vitro was unaltered in the presence of bacteria. These results suggest that vaginal microorganisms are unlikely to alter the natural history of HPV-associated CIN by influencing HPV oncogene expression.