Background The United Nations (UN) Convention on the Rights of Persons with Disabilities (CRPD) is a milestone in the recognition of the human rights of persons with disabilities, including the right to health and rehabilitation. South Africa has signed and ratified the CRPD but still has a long way to go in reforming policies and systems in order to be in compliance with the convention. This paper seeks to fill a gap in the literature by exploring what the barriers to the implementation of the health and rehabilitation articles of the CRPD are, as identified by representatives of the disability community. Methods This investigation used a qualitative, exploratory methodology. 10 semi-structured interviews of a purposive sample of representatives of disabled persons organizations (DPOs), non-governmental organizations (NGOs), and service providers in South Africa were conducted. Participants were drawn from urban, peri-urban, and rural settings in order to reflect diverse perspectives within South Africa. Data was analysed using a multi-stage coding process to establish the main categories and relationships between them. Results Six main categories of barriers to the implementation of the health and rehabilitation articles of the CRPD were identified. Attitude barriers including stigma and negative assumptions about persons with disabilities were seen as an underlying cause and influence on all of the other categories; which included political, financial, health systems, physical, and communication barriers. Conclusion The findings of this study have important implications for strategies and actions to implement the CRPD. Given the centrality of attitudinal barriers, greater sensitization around the area of disability is needed. Furthermore, disability should be better integrated and mainstreamed into more general initiatives to develop the health system and improve the lives of persons living in poverty in South Africa.