It has been suggested that vaginal lactobacilli may influence heterosexual transmission of HIV infection. The aim of this study was to compare the vaginal flora on Gram's stained and isolation rate, quantity and H2O2 production of lactobacilli between HIV positive and HIV negative women. Although, the prevalence of abnormal vaginal flora was increased in HIV infected women, there was no significant difference in isolation rate of vaginal lactobacilli between the two groups (71.87 vs. 83.33%; P>0.05). However, the results of this study showed significantly reduced quantity of lactobacilli in HIV infected women (P<0.01). In particular, the prevalence of H2O2-producing lactobacilli was lower in HIV positive as compared to HIV negative women (80 vs. 56.52%), with borderline significance (P=0.057). Taken together, our findings showed altered vaginal microflora with reduced quantity and hydrogen-peroxide production of vaginal lactobacilli in HIV positive women, but further studies are needed to assess its actual significance and potential benefit from the use of probiotic therapy.