Lactobacilli colonizing the rectum may be a reservoir for vaginal lactobacilli. In a cross-sectional study of 531 females, vaginal and rectal colonization by lactobacilli were assessed by culture methods. A subset of isolates was identified to the species level by use of whole-chromosomal DNA probes. Lactobacillus crispatus (16%), L. jensenii (10%), and L. gasseri (10%) were the prevalent lactobacilli colonizing the rectums of 290 females. Only 13 (9%) of 147 females colonized by L. crispatus or L. jensenii vaginally and/or rectally had bacterial vaginosis (BV), compared with 12 (44%) of 27 females colonized by other H(2)O(2)-producing lactobacilli (P < .001). Cocolonization of the vagina and rectum by H(2)O(2)-producing lactobacilli was associated with the lowest prevalence of BV (5%), whereas females colonized only vaginally, only rectally, or at neither site had a successively increased risk of BV (P < .001). Lactobacillus species in the rectum may contribute to the maintenance of vaginal microflora.