The aim of this study was to determine the reasons for delay of antiretroviral therapy (ART) in eligible HIV-infected children after the implementation of the South African National ART programme in April 2004, and to describe implemented interventions to improve ART access. This descriptive, retrospective audit included all HIV-infected children attending an ART clinic from April to December 2004, summarizing the following: (i) demographic data; (ii) HIV disease stage; (iii) CD4+ counts/percentages; (iv) ART eligibility and (v) reasons for ART delay. There were 276 study participants with a mean age of 4 years 4 months (range: 1 month–13 years). According to the South African national guidelines, 243 children were eligible for ART, but only 96 children were initiated on treatment during the study period, which was 39.5% of the eligible group and 34.8% of the total group. Important reasons for treatment delay were: (i) co-infection with tuberculosis (26.4%); (ii) lack of human resources (20.3%); (iii) socio-economic obstacles (17.3%) and (iv) incorrect disease stage classification (13.7%). Paediatric ART clinics need to co-operate closely with existing tuberculosis clinics for the effective management of tuberculosis co-infection; address socio-economic factors of HIV-affected families, especially the legal guardianship in orphans and improve their own staff capacity and the education of medical staff in HIV/AIDS management.