HIV-1 transmission in utero accounts for 20-30% of vertical transmission events in breast-feeding populations. In a prospective study of 463 HIV-1-infected mothers and infants, illness during pregnancy was associated with 2.6-fold increased risk of in-utero HIV-1 transmission [95% confidence interval (CI) 1.2-5.8] and bacterial vaginosis with a three-fold increase (95% CI 1.0-7.0) after adjusting for maternal HIV-1 viral load. Interventions targeting these novel risk factors could lead to more effective prevention of transmission during pregnancy.