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The epidemiology of sexually transmitted infections (STI) in rural, developing world populations is poorly understood. We estimated the prevalence and risk factors of Neisseria gonorrhoeae and Chlamydiatrachomatis in a female population in rural Nepal.We conducted a cross sectional study in a sample of 1177 postpartum women participating in a micronutrient supplementation trial in Nepal. Urine samples were collected to test for the two infections using the ligase chain reaction (LCR).C trachomatis was detected in 1.0% (95% confidence intervals (CI): 0.4 to 1.5) and N gonorrhoeae in 2.3% (95% CI: 1.2 to 3.4) of women. None of the women tested positive for both. Self report of all three symptoms of lower abdominal pain, pain and burning on urination, and vaginal discharge was associated with the presence of gonorrhoea (odds ratio (OR): 12.1, 95% CI: 1.3 to 115.0). Neonatal eye discharge was associated with maternal gonococcal infection (OR = 5.2, 95% CI: 1.1 to 24.9). Incidence of low birth weight was not related to these maternal infections, but very preterm delivery (<32 weeks) was higher among women positive for gonorrhoea (OR = 4.7, 95% CI: 1.0 to 22.0). In a multivariable analysis, low body mass index (<18.5) and cattle ownership were associated with gonorrhoea (p <0.05), whereas woman’s literacy was associated with chlamydia (p = 0.06).We found the rates of N gonorrhoeae and C trachomatis to be low among women in this rural population of Nepal.