OBJECTIVE The goals of this study were as follows: (1) to further define the microbiologic characteristics of bacterial vaginosis in nonpregnant women, (2) to evaluate the in vivo activity of topical intravaginal clindamycin and reference this activity to clinical cure, and (3) to evaluate for clindamycin-related emergence of species. METHODS Vaginal microflora was identified and quantified from 33 women with bacterial vaginosis at enrollment and 4 to 7 days after treatment with placebo or three different dosages of clindamycin administered twice daily for 5 days in a double-blind, randomized trial. RESULTS Clindamycin eradicated and/or decreased counts of major bacterial vaginosis-associated microflora such as Gardnerella, gram-negative and gram-positive anaerobes, and Mycoplasma hominis; this was correlated with cure in 22 of 24 (92%) women. Altered flora (nonlactobacilli) among some of the women who received clindamycin appeared to be transient and without apparent adverse effects. CONCLUSIONS Microbial (and clinical) results support use of clindamycin as effective treatment of bacterial vaginosis.