The microbial contamination of the female genital tract has effect on the ivf outcome and negatively effect on fertility, fertilization and implantation rate. Lactobacillus sp. is the dominant organism of the vaginal flora that have an important role in the inhibition of pathogen. 48 patients were selected for this study aged between 20-40 years, During embryo transfer, 3 samples were collected from each patient from vagina, end cervical canal and the tip of the catheter. The samples were assayed microbiology. The microbial culture contained natural flora and pathogen organism .The isolated pathogens were identified as Klebsilla pneumonia, Escherichia coli, Candida albicans, C. tropicalis, C. famata, C. parapsilosis, C. catenulate according to Bergeyˊs manual and confirmed by VITEK System. Candida sp found to be the most frequent infemale genital tract. The probiotic (Lactobacillus. acidophilus) and its metabolites (bacteriocin) were inhibited growth of isolated pathogenic microbial  in vitro.The result showed that L. acidophilus and their metabolite bacteriocin have antagonistic activity against pathogenic microbes.
                Recommendation: Oral or transvaginal administration of Lactobacillus or bacteriocin antiseptics; disinfected; maintain a health vagina and prevent the infection of the reproductive tract.