Lactobacilli constitute an important part of the normal indigenous alimentary and urogenital tract microbiota of man and animals. The indigenous microbiota is a natural resistance factor against potential pathogenic microorganisms and provides colonization resistance by promoting gut maturation and integrity, steric exclusion, producing autogenic regulation factors (e.g. organic acids, hydrogen peroxide and bacteriocins). Lactobacilli thus play an important role in maintaining vaginal health of women (1) and form the dominant species of the vaginal microbiota (2). When lactobacilli are depleted due to douching, sexual practice and use of antibiotics, other pathogenic organisms such as Gram-negative anaerobes take over and it results in bacterial vaginosis (BV) (3) which is the commonest cause of vaginal discharge occurring in women attending gynaecological clinics in our country. The adverse effects of BV on pregnancy and acquisition of HIV are enormous to women (4). The hydrogen peroxide producing lactobacilli may have a protective role against vaginal colonization by pathogenic species such as those causing BV and possibly human immunodeficiency virus (HIV), gonorrhoea and herpes simplex virus-2 (5,6). There is therefore growing interest in use of lactobacilli of human origin as probiotics against genital infections. In the development of appropriate biotherapeutic remedy for these conditions, such as probiotic lactobacilli and vaccine development, the identification of the dominant vaginal lactobacilli present is vital. In recent years there have been significant advances in the characterization and identification of bacteria by molecular methods. Especially, Lactobacillus species that are commensals in the human vagina have received considerable attention as a result of their probiotic properties (7). The new culture-independent techniques, such as pulse field gel electrophoresis (PFGE), ribotyping, 16S rDNA restriction fragment length polymorphism (RFLP), multiplex polymerase chain reaction (PCR), arbitrary primed (AP) PCR or triplet arbitrary primed (TAP) PCRs, provide more specific methods for detailed investigations at the species and the strain levels and are valuable tools for ecological Lactobacillus studies as well.