The extent of the HIV pandemic — particularly in the hardest-hit countries, including South Africa — has prompted a call for greater engagement of all groups, including faith-based organisations (FBOs). Although FBOs are known to play a substantial role in providing care and support to those affected by HIV and AIDS, empirical evidence in regard to their actions in the broader context of stigma is limited. A qualitative, key-informant survey was conducted in South Africa as part of a six-country international study to examine perceptions of how FBOs have contributed to reduction in HIV risk, vulnerability and related impacts. The special emphasis of this paper is the influence of FBOs on stigma and discrimination. In-depth interviews were held with 34 senior-level key informants who act as key decision-makers in the response to HIV and AIDS in South Africa. Secular and faith-based respondents shared their perceptions of the faith-based response, including FBOs' actions in relation to HIV/AIDS stigma and discrimination. Our study revealed that while FBOs were perceived as taking some action to address stigma in South Africa, FBOs were also thought to contribute to HIV/AIDS- discrimination through conflating issues of sexuality and morality, and through associating HIV and AIDS with sin. The interviewees indicated a number of internal and external challenges faced by FBOs to deal effectively with stigma, including lack of information and skills, the difficulty of maintaining confidentiality in health services, and self-stigmatisation which prevents HIV-infected persons from revealing their status. Findings from this study may help both faith-based and secular groups capitalise on the perceived strengths of FBOs as well as to elucidate their perceived weaknesses so that these areas of concern can be further explored and addressed.