This study assesses the UN Inter-agency Group for Child Mortality Estimation (IGME) methods of estimating the infant and neonatal mortality rates from the under-five mortality rates in countries affected by HIV/AIDS. It uses Botswana, Malawi and South Africa as case studies. The assessment is made by comparing the IGME results with estimates from projection models and empirical results computed from survey data and vital statistics data corrected for the level of incompleteness for the countries included in the study. In addition, relevant literature is reviewed in order to determine the reasonableness and impact (on the results produced) of the assumptions made by the method.