BACKGROUND: An integrated chronic disease management (ICDM) model was introduced by the National Department of Health in South Africa to tackle the dual burden of HIV/AIDS and non-communicable diseases. One of the aims of the ICDM model is to reduce HIV-related stigma. This paper describes the viewpoints of service users and providers on HIV stigma in an ICDM model in rural South Africa. MATERIALS AND METHODS: A content analysis of HIV stigmatisation in seven primary health care (PHC) facilities and their catchment communities was conducted in 2013 in the rural Agincourt sub-district, South Africa. Eight Focus Group Discussions were used to obtain data from 61 purposively selected participants who were 18 years and above. Seven In-Depth Interviews were conducted with the nurses-in-charge of the facilities. The transcripts were inductively analysed using MAXQDA 2018 qualitative software. RESULTS: The emerging themes were HIV stigma, HIV testing and reproductive health-related concerns. Both service providers and users perceived implementation of the ICDM model may have led to reduced HIV stigma in the facilities. On the other hand, service users and providers thought HIV stigma increased in the communities because community members thought that home-based carers visited the homes of People living with HIV. Service users thought that routine HIV testing, intended for pregnant women, was linked with unwanted pregnancies among adolescents who wanted to use contraceptives but refused to take an HIV test as a precondition for receiving contraceptives. CONCLUSIONS: Although the ICDM model was perceived to have contributed to reducing HIV stigma in the health facilities, it was linked with stigma in the communities. This has implications for practice in the community component of the ICDM model in the study setting and elsewhere in South Africa.