Objectives: Vaginal pH is related to hormonal status, and adolescents experience disturbed hormonal patterns following menarche. We assessed hormonal factors and risk of abnormal vaginal pH and bacterial vaginosis (BV) among adolescents attending genitourinary medicine (GUM) clinics. Methods: In a cross sectional study adolescents within 5 years of menarche, (17 years, or with oligoamenorrhoea were recruited. Vaginal pH and BV were assessed and among those not using hormonal contraceptives, estrone-3-glucuronide (E3G) and pregnanediol-3a-glucuronide (P3G) concentrations were measured. Results: Among 102 adolescents, 59.8% (61) had a high vaginal pH (.4.5), which was higher than the prevalence of BV, detected in 33% (34). No association was found between presence of sexually transmitted infections (STI) and vaginal pH. In logistic regression, after controlling for BV and condom use, vaginal pH was positively associated with cervical ectopy (OR = 2.5; 95% CI 1.0 to 6.6, p = 0.05) and STI treatment history (OR = 2.5; 95% CI 0.9 to 6.5, p = 0.07), and negatively associated with use of DepoProvera (OR = 0.1; 95% CI 0.03 to 0.6, p = 0.003) and recent onset (,12 months) of sexual activity (OR = 0.2; 95% CI 0.1 to 0.7, p = 0.004). Among 23 adolescents not using hormonal contraceptives, a high pH occurred more often in abnormal compared to normal menstrual cycles (OR = 10.8; 95% CI 1.4 to 85.4; p = 0.026). E3G concentrations were inversely correlated with vaginal pH in the follicular phase (Spearman: r = 0.51; p = 0.024). Conclusions: Ectopy and abnormal menstrual cycles are common features of adolescence. Their presence is associated with increased risk of abnormal pH, and may also predispose to BV.