Bacterial vaginosis (BV) is characterized by dramatic changes in the vaginal ecosystem. Women without evidence of vaginal infection may exhibit transient changes in their flora. We prospectively followed up women by using diaries and self-obtained vaginal smears to correlate behaviors with changes in flora. The majority of women (38/51, 78%) had significant, although transient, changes. Behaviors associated with unstable flora were a history of BV, a greater number of partners, and more frequent episodes of receptive oral sex. Only the latter remained significantly associated in the multivariate analysis. Variables that were associated with day-to-day variability in the flora included use of vaginal medication, menses, greater number of partners, spermicide use, more frequent vaginal intercourse, and less frequent use of condoms. Only a minority of women (11/51, 22%) maintained a “normal” lactobacillus-predominant flora. Factors associated with instability of the flora are similar to those epidemiologically associated with BV.