Objective Most of the HIV pediatric infections are acquired through mother-to-child transmission (MTCT). Porto Alegre is a state capital of Brazil that had a HIV MTCT rate of 4.1% in 2013 and the highest rate of HIV-infected pregnant women in the country during 2018. Zidovudine and nevirapine have been used in Brazil for high-risk newborns since 2012. The aim of the study was to investigate HIV MTCT rate and the factors associated with HIV transmission at a hospital that is a reference center for HIV-infected mothers in Porto Alegre, after the introduction of this policy. Study Design This retrospective cohort study included all HIV-exposed infants born between February 2013 and December 2016 at the Hospital de Clínicas de Porto Alegre. Student's t-test or Fisher's exact test was used to compare variables between HIV-infected and uninfected groups of newborns. Poisson's regression with robust variance was used to determine the factors associated with HIV MTCT. Results A total of 375 newborns were exposed to HIV, with an outpatient loss of 14.4% (n = 54). The HIV MTCT rate was 2.18% (n = 7), with four infected during the intrauterine period. The risk factors for MTCT were no prenatal care (relative risk [RR] = 9.4; 95% confidence interval [CI]: 2.0–44.3), late maternal HIV diagnosis in the peripartum period (RR = 16.3; 95% CI: 3.6–73.0), syphilis infection during pregnancy (RR = 9.3; 95% CI: 2.1–40.3), maternal viral load >1,000 copies/mL in the third trimester or peripartum period (RR = 9.5; 95% CI: 1.7–50.5), and lack of or inappropriate antiretroviral therapy during pregnancy (RR = 8.2; 95% CI: 1.6–41.4). Conclusion MTCT rate was 2.18%. With the institution of two-drug prophylaxis for high-risk newborns, persistent cases HIV MTCT were predominantly found among women with absence of antenatal care, late HIV diagnosis, syphilis coinfection, high viral load, and inadequate ARV therapy during pregnancy. Although zidovudine and nevirapine were administered postnatally to high-risk newborns, this regimen could not prevent transplacental transmission. Key Points