Despite antiretroviral therapy rollout in South Africa, fewer children than expected are accessing HIV care services. Our objectives were to describe barriers and facilitators of uptake of HIV care among children. Our study involved six private-sector clinics which provide HIV care free-of-charge in and around Gauteng province, South Africa. In-depth interviews were conducted in July 2008 with 21 caregivers of HIV-infected children attending these clinics, 21 clinic staff members and three lead members of staff from affiliated care centres. Many children were only tested for HIV after being recurrently unwell. The main facility-related barriers reported were long queues, negative staff attitudes, missed testing opportunities at healthcare facilities and provider difficulties with paediatric counselling and venesection. Caregivers reported lack of money for transport, food and treatments for opportunistic infections, poor access to welfare grants and lack of coordination amongst multiple caregivers. Misperceptions about HIV, maternal guilt and fear of negative repercussions from disclosure were common. Reported facilitators included measures implemented by clinics to help with transport, support from family and day-care centres/orphanages, and seeing children's health improve on treatment. Participants felt that better public knowledge about HIV would facilitate uptake. Poverty and the implications of children's HIV infection for their families underlie many of these factors. Some staff-related and practical issues may be addressed by improved training and simple measures employed at clinics. However, changing caregiver attitudes may require interventions at both individual and societal levels. Healthcare providers should actively promote HIV testing and care-seeking for children.