Abstract: Objective To investigate the change of intestinal flora in subjects receiving oral vaccination with inactivated whole-cell/recombinant B subunit (WC/rBS) O₁₃₉ cholera vaccine made in China. Methods The fecal smears of 5 groups of subjects receiving the vaccine were collected before and 2 and 3 months after the vaccination to examine the distribution of the intestinal flora. Results In the 458 specimens examined, the total amount of bacteria and percentages of G⁺b, G⁺c and G^-c were decreased whereas the amount of G^-b significantly increased after vaccination. Compared with the placebo control group, the vaccinated groups exhibited significant changes in G⁺b and G^-c, which also varied significantly between the group receiving 3 doses of WC/rBS vaccine and the other vaccinated groups. The vaccination produced distinct changes in the percentage of the intestinal flora at different time points, showing the most obvious effect on G^-b. Oral vaccination was shown to affect the percentage of the intestinal flora very likely through its effect on the amount of G^-b. The percentages of G⁺b, G^-b and G^-c varied significantly between male and female subjects after vaccination. Conclusion Oral vaccination with WC/rBS affects the intestinal flora in human, and the mechanism as well as the implications needs to be further explored.