Antiretroviral therapy (ART) in pregnancy was associated with a drastic reduction in HIV mother-to-child transmission (MTCT), although it was associated with neonatal adverse effects. The aim of this study was to evaluate the neonatal effects to maternal ART. This study was a cohort of newborns from HIV pregnant women followed at the CAISM/UNICAMP Obstetric Clinic from 2000 to 2015. The following adverse effects were evaluated: anemia, thrombocytopenia, liver function tests abnormalities, preterm birth, low birth weight and congenital malformation. Data collected from patients' files was added to a specific database. Descriptive analysis was shown in terms of absolute (n) and relative (%) frequencies and mean, median and standard deviation calculations. The association between variables was tested through Chi-square or Fisher exact test (n < 5) and relative risk (RR) with its respective p values for the categorical ones and t-Student (parametric data) or Mann-Whitney (non-parametric data) for the quantitative ones. The significant level used was 0.05. A multivariate Cox Logistic Regression was done. Statistical analysis was performed using SAS version 9.4. Data from 787 newborns was analyzed. MTCT rate was 2.3%, with 0.8% in the last 5 years. Observed neonatal adverse effects were: liver function tests abnormalities (36%), anemia (25.7%), low birth weight (22.5%), preterm birth (21.7%), children small for gestational age (SGA) (18%), birth defects (10%) and thrombocytopenia (3.6%). In the multivariate analysis, peripartum CD4 higher than 200 cells/mm was protective for low birth weight and preterm birth, and C-section was associated with low birth weight, but not with preterm birth. Neonatal anemia was associated with preterm birth and exposure to maternal AZT. Liver function tests abnormalities were associated with detectable peripartum maternal viral load and exposure to nevirapine. No association was found between different ART regimens or timing of exposure with preterm birth, low birth weight or congenital malformation. Highly active antiretroviral treatment in pregnant women and viral load control were the main factors associated with MTCT reduction. Antiretroviral use is associated with a high frequency but mainly low severity adverse effects in newborns.