The prevalence of genital shedding of herpes simplex virus (HSV)-2 and related risk factors was evaluated in a prospective population of 355 women attending the Maternity Joséphine Bongo, in Libreville, Gabon. We found a high prevalence (66%) of HSV-2 seropositivity, with a high proportion, 14%, of women harbouring HSV-2 DNA shedding in their genital secretions. HSV-2 genital shedding was positively associated with previous episodes of genital blisters, current genital ulcer, current genital blister, HIV seropositivity and HSV-2 seropositivity. The high prevalence of HSV-2 in childbearing-aged population indicates that young women living in Gabon are at high risk for HIV acquisition in HIV-seronegative women sexually exposed to HIV, for HIV transmission in HIV-infected women co-infected by HSV-2 and finally for HSV-2 vertical transmission during pregnancy.