As of 2012, only 34% of treatment eligible children in low- and middle-income countries were receiving antiretroviral treatment (ART) despite proven benefits of early initiation of antiretroviral treatment (ART) on child survival. We reviewed routine EID (early infant diagnosis) laboratory and paediatric ART patient records to determine missed opportunities for optimizing EID and current status of linkage between EID entry points to paediatric ART initiation in Tanzania, Uganda, and Zimbabwe. These are three countries with EID coverage of 22, 11 and 14%, respectively and ART coverage rates of 18, 16 and 32%, respectively. This article examines the most likely delivery points for collection of blood samples for EID testing for infant and young children and the most likely referral points for ART initiation of HIV-infected children in these three countries. This data provides evidence of consistent missed opportunities for linking HIV-infected children identified during EID to early ART treatment. We also argue for expanding the provision of EID to other service delivery points beyond PMTCT platform and provide suggestions for better linkages from EID to care and treatment.