Vaginal microbiota is an important early source of bacterial colonization for newborns. However, only a few small studies have investigated the composition of vaginal microbiota during labor. In this work, we analyzed vaginal swabs collected at 36 weeks gestation and at the onset of labor from 256 women participating in a randomized placebo-controlled study of probiotic supplementation for the prevention of atopic dermatitis in offspring. Although individuals' vaginal microbiota was stable over time, several bacterial families, which are characteristic of mixed community state type (CST) IV, were overrepresented in vaginal swabs sampled at labor. Alpha-diversity also tended to increase by between 36 weeks gestation and the onset of birth. In the majority of women, CST remained the same throughout the study. Among the women who switched their vaginal microbiota from one CST to another, approximately half shifted towards CST IV. Although CST IV is often associated with bacterial vaginosis, which in turn may lead to preterm birth, in our cohort this shift was not associated with self-reported vaginosis, preterm delivery or birthweight. Probiotic consumption did not alter vaginal microbiota.