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Large datasets for investigating vaginal flora change at frequent, repeated intervals are limited and graphical methods for exploring such data are inadequate. We report 2-year weekly vaginal flora changes based on Gram stain using lasagna plots.Weekly vaginal flora patterns were evaluated among 211 sexually experienced women with ≥18 months of follow-up in Rakai, Uganda. Vaginal flora swabs were self-collected weekly and categorized by Nugent Gram stain criteria (0–3, normal; 4–6, intermediate; 7–10, bacterial vaginosis [BV]). Vaginal flora patterns were analyzed as the percentage of weekly observations with BV (longitudinal prevalence) and illustrated by lasagna plots. Characteristics of women were compared across tertiles of longitudinal prevalence of BV.Ninety-five percent of women had at least 1 episode of BV over 2 years, with one-third of women spending more than half (52%–100%) of their time with BV. Vaginal pH >4.5 increased with increasing tertiles of longitudinal prevalence of BV (P < 0.001). Weekly fluctuation in vaginal flora states, as measured by a change in flora states from the before current visit, was highest in the middle (41.9%) compared with the lower (30.1%) and upper tertiles (27.8%, P < 0.001). HIV status and reported vaginal symptoms did not differ significantly across BV tertiles.Women exhibited different patterns of vaginal flora changes over time, which could not be described by baseline behaviors. Lasagna plots aided in describing the natural history of BV within and across women and may be applied to future BV natural history studies.