Background: South African young women continue to be vulnerable, with high prevalence of teenage pregnancy, HIV, sexually transmitted infections (STIs) and female genital schistosomiasis (FGS). This study seeks to examine the underlying factors that may be associated with these four adverse reproductive health outcomes. Methods: In a cross-sectional study of 1413 sexually active of young women, we explored these four adverse reproductive health outcomes by considering socio-demographic factors, socio-economic factors, sexual risk behaviour, substance abuse and knowledge about reproductive health by using a questionnaire. Consenting participants were asked about previous pregnancies and were tested for HIV, STIs and FGS. Multivariable regression analyses were used to explore the factors associated with these four reproductive health outcomes. Results: 1. Early pregnancy: Among the young women, 44.4% had already been pregnant at least once. Associated factors were hormonal contraceptives, (adjusted odds ratio (AOR): 17.94, 95% confidence interval (CI): 12.73-25.29), and sexual debut < 16 years (AOR: 3.83, 95% CI: 2.68-5.47). Living with both parents (AOR 0.37, 95% CI: 0.25-0.57) and having a steady partner (AOR: 0.43, 95% CI: 0.24-0.76) were identified as protective factors against pregnancy. 2. HIV: HIV prevalence was 17.1%. The odds of having HIV were higher in intergenerational (AOR: 2.06, 95% CI: 1.05-4.06) and intragenerational relationships (AOR: 1.51 95% CI: 1.06-2.15), compared to age-homogenous relationships. Other associated factors were: condom use (AOR: 1.60, 95% CI: 1.16-2.20), number of times treated for an STI (AOR: 1.32, 95% CI: 1.02-1.71), and total number of partners (AOR: 1.14, 95% CI: 1.03-1.28). 3. STIs: Participants who had at least one STI (40.5%) were associated with total partner number (AOR 1.17, 95% CI: 1.06-1.30), and testing HIV positive (AOR: 1.88, 95% CI 1.41-2.50). 4. FGS: FGS prevalence (19.7%) was associated with previous anti-schistosomal treatment (AOR: 2.18, 95% CI: 1.57-3.05). Conclusion: There is a high prevalence of pregnancy, HIV, STIs and FGS among sexually active young women in rural KwaZulu-Natal. Multidisciplinary approaches are urgently needed for educational and health literacy programs prior to sexual debut, and health care facilities, which should be made accessible for young women.