OBJECTIVE: The objective of this study was to determine whether Lactobacillus species found in African women differ substantially to those of Caucasian decent, described in previous studies. The vaginal microbiota play an important role in female health, and when the naturally dominant lactobacilli are displaced resulting in bacterial vaginosis (BV), the host is more at risk of acquiring sexually transmitted diseases, including HIV. METHODS: Vaginal samples were collected from 241 healthy, pre-menopausal Nigerian women, which were then Gram stained for Nugent scoring. Microbial DNA was extracted, amplified using PCR and Lactobacillus primers, and processed by Denaturing Gradient Gel Electrophoresis (DGGE). Lactobacillus species were identified by DNA sequencing and BLAST algorithm. RESULTS: Of the samples, 207 (85.8%) had PCR products for lactobacilli, while 34 (14.2%) showed absence of lactobacilli which correlated to the BV Nugent scores. Upon sequencing of amplicons, 149 subjects (72%) had sequence homologies to lactobacilli. Most women (64%) were colonized by L. iners as the predominant strain similar to previous findings in Canadian and Swedish women. L. gasseri was found in 7.3% samples, followed by L. plantarum, L. suntoryeus, L. crispatus, L. rhamnosus and other species. CONCLUSION: The findings indicate that even with geographical, racial and other differences, the predominant vaginal Lactobacillus species is similar to species in women from Northern countries.