Background: Women, especially in developing countries, most often bear the brunt of HIV infections. The continued lack of viable vaccines and microbicides has made some women resort to using natural products such as lemon or lime juice to avoid infection. Few in vitro studies have been done on the effect of lemon juice on vaginal cells and lactobacilli that constitute the major microbiota in healthy women. Objective: The objective of the present study was to evaluate in vitro the effect of lemon juice on the viability of vaginal cells (VK2/E6E7) and vaginal Lactobacillus species. Methods: Vaginal cells were exposed to different concentrations (0–30%) of lemon juice at pH 2.3 and 4.5 for 10 min. Viability was determined by staining the cells with propidium iodide and analysing them by flow cytometry. Lactobacillus organisms were dispensed into microplates with vaginally defined medium + peptone (VDMP) containing different concentrations of lemon juice ranging from 0 to 100%. Results: Lemon juice at pH 2.3 had a significant (P = 0.03) toxic effect on the vaginal cell line used. At 30% concentration, the vaginal cells were practically non-viable, typified by a 95% loss of viability, whereas at pH 4.5 there was only 5% cell loss. Lemon juice had varying growth inhibitory effects on the Lactobacillus species tested. At pH 4.5 and using 10–30% lemon juice, there was a stimulatory growth effect on certain Lactobacillus species. Conclusions: Lemon juice (20–30%) at pH 2.3 was highly toxic to VK2/E6E7 cells, and at pH 4.5 there was no significant effect on the viability of the cells within 10 min. Lemon juice above 10% at pH 2.3 was found to be detrimental to the growth of vaginal lactobacilli. Although lemon juice may be useful in other applications, its use in the vaginal region should be discouraged.