Background A majority of HIV-infected children die by two years of age without antiretroviral therapy (ART). Unfortunately, diagnosing HIV in this age group is complex as it requires virologic testing. This has served as a barrier to younger HIV-infected (HIV+) children accessing ART in resource-constrained generalized epidemic countries. Malawi, a high HIV-prevalence country in sub-Saharan Africa, implemented a national early infant diagnosis (EID) program utilizing virologic testing with dried blood spots (DBS) DNA PCR technology in 2007 to address this gap.