Background : Bacterial vaginosis (BV) is a common infection in reproductive age of women and associated with preterm birth and premature rupture of membrane (PROM). Both clindamycin and metronidazole can be used to treat bacterial vaginosis in pregnancy.Aim : To analyze medical characteristics and comparison of clindamycin and metronidazol for treatment of bacterial vaginosis in pregnancy.Methods : This was a study of non randomized clinical trial. Fifty-six pregnant women were identified and including 19 women were evaluated. Six pregnant received clindamycin and 13 received metronidazole then Mann Whitney test was used to analyze.Results : Age of subjects, age of pregnancy, history of abortus, prematurity, PROM and used of contraception were no significant difference with incidence of BV infection (p=0,548, p=0,739, p=0,505, p=0,088, p=1,000, p=0,867). But symptoms and parity were significantly associated with incidence of BV infection (p=<0,001, p=0,047). There was no significant difference in score of Lactobacillus, Gardnerella, Mobiluncus, and total score after treatment between clindamycin and metronidazole (p=1,000, p=1,000, p=0,564, p=0,564).Conclusion : Symptoms and parity was associated with BV infection. Means of Mobiluncus and total score after treatment of metronidazole were lower than clindamycin, but there was no significant difference in score Lactobacillus, Gardnerella, Mobiluncus and total score between clindamycin and metronidazole after treatment.