Background: In South Africa, current estimates indicate that 1% of infants will be HIV PCR-positive by 2 months of age. WHO recommends early infant diagnosis (EID) and immediate initiation of antiretroviral therapy (ART) in infants who are diagnosed with HIV infection within the first year of life. Aims: To investigate rates of EID and subsequent ART initiation in infants attending the Primary Health Care (PHC) clinics which fed Mseleni Hospital during 2012. Objectives: To measure the number of infants (<1 year of age) testing HIV PCR-positive who are currently collecting ART and those lost to follow-up. Methods: IV PCR test results from Mseleni Hospital in 2012 were cross-referenced with the national database (TIER.net) for ART initiation and follow-up from the National Health Laboratory Service (NHLS) database. Results: 455 of 843 (54%) HIV-exposed infants (<2 months) were tested by HIV PCR, 11 of whom (2·4%) tested positive, reflecting the national prevalence. Of 897 HIV PCR tests undertaken in infants <1 year, 51 (5·7%) were positive, and 36 were included for analysis. Only 13 (36·1%) of these infants are currently collecting ART; seven (19·4%) commenced ART but were lost to follow-up, and 16 (44·5%) never started ART. Conclusion: 16 (44·5%) HIV PCR-positive infants in Mseleni Hospital and its feeder PHCs were not commenced on ART. This may reflect a similar problem in other rural hospitals in South Africa. Specific interventions are required to rapidly up-scale early initiation of ART in this vulnerable group of infants.