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Sexually transmitted infections (STIs) in Madagascar have primarily been monitored in selected groups of patients attending STI clinics in major cities as part of the HIV surveillance program in Madagascar.The aim of the study was to provide complementary data related to STI prevalence in a general rural population.STIs were investigated in 643 subjects aged 15 to 49 years as part of a cross-sectional morbidity study of urogenital schistosomiasis. Infection rates were reassessed 3 weeks and 6 months after systematic STI treatment at baseline.Neisseria gonorrhoeae (Ng), Chlamydia trachomatis (Ct), Mycoplasma genitalium (Mg), Trichomonas vaginalis (Tv), and/or antibodies to Treponema pallidum (Tp) were diagnosed in 125 (37.5%) of 333 women and in 83 (26.8%) of 310 men. In addition, 49% of the women and 28% of the men were infected with herpes simplex virus-2. Six (0.9%) subjects were found HIV-antibody positive. Between the 3-week and 6-month follow-up surveys Ng, Ct, and/or Mg prevalence increased most prominently in women aged 15 to 24 years.Study findings suggest that rural areas in Madagascar should be as closely monitored and assisted in STI and HIV control as their urban counterparts. Following the current consensus, young adults should constitute a priority target group in the control programs.