Abstract In South Africa, a third of children born are exposed to HIV, while fewer undergo an HIV confirmatory test. Anti-retroviral therapy (ART) coverage among children remains low-despite roll-out of the national ART programme in South Africa in 2004. This study sought to understand critical barriers to seeking HIV-related care for children in rural South Africa. Data presented in this article derive from community-based qualitative research in poor rural villages in north-east South Africa; this includes 21 in-depth interviews in 2008 among caregivers of children identified as HIV-positive in 2007 from a randomly selected community-based sample. Using NVIVO 8, data were coded and analysed, using a constant comparative method to identify themes and their repetitions and variations. Structural barriers leading to poor access to health care, and social and systems barriers, all influenced paediatric HIV treatment seeking. Of concern was the expressed need to maintain secrecy regarding a child's HIV status to avoid stigma and discrimination, and misconceptions regarding the course of HIV disease in children; this led to a delay in seeking appropriate care. These barriers need to be addressed, including through focused awareness campaigns, improved access to health care and interventions to address rural poverty and development at both household and community levels. In addition, training of health care professionals to improve their attitudes and practice may be necessary. However, this study only provides the perspective of the caregivers; further studies with health care providers are needed to gain a fuller picture for appropriate policy and practice guidance.