Full study dataset.

Although antiretroviral therapy (ART) scale up has markedly lowered vertical transmission, the relative contribution of ART regimens, maternal factors, and infant practices within Prevention of vertical transmission (PVT) programs is not fully understood. We assessed the comparative influence of maternal and infant factors on infant HIV positivity. We retrospectively reviewed records of 962 HIV exposed infants attending the Mildmay Uganda PVT clinic between 2018 and 2023. Of these, 918 were mother-infant pairs. Descriptive statistics summarised maternal and infant characteristics. Associations were assessed using Chi square or Fisher exact tests. Two independent logistic regression models identified infant and maternal factors associated with HIV positivity. Pseudo R² evaluated model performance and area under the curve measured discrimination. Among 918 mother-infant pairs, HIV positivity was 1.96% (18). PI based regimens were associated with increased odds of HIV positivity (aOR 22.89, 95% CI 2.20–238.14, p = 0.009). Among maternal factors, HIV positivity differed significantly by age group (p