INTRODUCTION: While the rate of vertically transmitted HIV infection has fallen in most regions of Brazil, there have been no similar decreases in northern and northeastern Brazil. OBJECTIVE: The objective of this study was to evaluate the risk factors associated with vertical transmission in the state of Sergipe in northeastern Brazil. METHODS: This was a retrospective cohort study. We recorded clinic and registry data for all HIV-infected pregnant women and exposed children diagnosed in Sergipe from 1990 to 2011. RESULTS: We identified 538 deliveries and 561 HIV-exposed infants (23 sets of twins). One hundred one (18.9%) infants were HIV-infected. In the multivariate analysis, infant antiretroviral prophylaxis was a significant protective factor (adjusted odds ratio (aOR) 0.07, 95% confidence interval (CI) 0.01-0.41, p=0.003). Breastfeeding was marginally associated with an increased odds of perinatal transmission (aOR 4.52, 95% CI 0.78-26.17, p = 0.092). The attributable risk percentage for breastfeeding over the study period was 91.0%. Transmission decreased from 91 per 100 live births before 1997 to 2 per 100 in 2011 following the adoption of the prevention protocol. CONCLUSION: Transmission declined over the study period. The screening of pregnant women and timely initiation of prophylaxis and therapy are issues that require further attention.