Background: This study aimed to assess the effects of maternal bacterial vaginosis (BV) on the morbidity and mortality of HIV-exposed infants of women enrolled in a randomized controlled trial (pre-dating antiretroviral therapy) at birth, 6 months, and 12 months. Methods: Four hundred and twenty-five HIV-positive pregnant women were enrolled in this trial and were categorized as exposed if they had a laboratory-based diagnosis of BV (Nugent method). We compared the morbidity and mortality of infants of the mothers at birth, 6 months, and 12 months. We assessed morbidities from the mother’s history and clinical examination during scheduled and non-scheduled visits. The data that were collected longitudinally were then analyzed via multiple logistic regression with the generalized estimating equation. An independent correlation structure was assumed to evaluate the specific morbidity risks to infants associated with exposure to BV. We used the Kaplan–Meier method to generate the cumulative hazard curve, to determine mortalities at different stages between the two groups. Overall, only data for 328 infants were complete and used in the analysis.Results: Data were available for 159 and 171 BV exposed and non-exposed mothers, respectively. Exposure to BV was not associated with any neonatal morbidity at birth, but was associated with adverse maternal condition (unadjusted odds ratio [OR], 2.93; 95% confidence interval [CI], 1.19–7.20, P=0.02) and maternal hospital admissions (unadjusted OR, 1.95; 95% CI, 1.08–3.51, P=0.02). At 6 months, infants of BV exposed mothers had higher odds of bloody stool (adjusted OR, 3.08; 95% CI, 1.11–10.00, P=0.04), dehydration (adjusted OR, 2.94; 95% CI, 1.44–6.37, P=0.01), vomiting (adjusted OR, 1.64; 95% CI, 1.06–2.56, P=0.03), and mouth ulcers (adjusted OR, 12.8; 95% CI, 2.27–241.21, P=0.02). At 12 months, exposure to BV was associated with dehydration (adjusted OR, 1.81; 95% CI, 1.05–3.19, P=0.03) and vomiting (adjusted OR, 1.39; 95% CI, 1.01–1.92, P=0.04). Kaplan–Meier survival analysis showed no association of BV with infant mortality (P=0.65); however, the cumulative hazard curve showed a higher trend toward deaths among BV exposed infants.Conclusion: Our findings demonstrate that BV is a good predictor of maternal and infant morbidities. Infants of both HIV and BV exposed mothers can manifest these symptoms at any stage within a year of growth. Adverse maternal condition and hospitalization of mothers after birth could indicate exposure to BV. Bloody stool, dehydration, vomiting, and mouth ulcers could indicate exposure to BV among infants.