BACKGROUND: Youth in South Africa have been identified as a high-risk group for contracting HIV. In response, the South African Integrated School Health Policy (ISHP) has been developed with the aim of guiding the provision of comprehensive healthcare services within South African schools. Accordingly, the scale-up of HIV counselling and testing (HCT) in high schools is a priority. This study examines the factors affecting the utilisation of HCT services amongst learners in high schools in the KwaZulu-Natal province of South Africa. METHODS: Focus group discussions were conducted in 12 rural schools in the Vulindlela sub-district of uMgungundlovu in KwaZulu-Natal. A total of 158 randomly selected learners took part, aged 16 years and older from grades 10, 11 and 12. Qualitative analysis was conducted using the framework approach, providing a systematic structure allowing for a priori and emergent codes, with social cognitive theory as a theoretical framework. RESULTS: The stigma and discrimination attached to testing, along with the inherent fear of a positive result were the biggest barriers to HCT uptake. Fear and the subsequent negative beliefs around HCT were borne out of insufficient knowledge. These fears were exacerbated by the perceived or real attitudes of peers, partners and family towards HIV. The prospect of a positive result and the possible resultant societal backlash hinders high and regular uptake of HCT. Stigma and discrimination remain the foremost barriers to HIV testing despite the presence of localised and convenient testing. Interventions aimed at addressing these challenges could increase the demand for HIV testing amongst adolescents. CONCLUSIONS: Increasing education about the importance of HCT and creating awareness about available HCT services will not be enough to increase uptake in schools in South Africa. Efforts to decrease stigma around HIV and HCT by integrating testing into general and sexual reproductive health services offered to youth, and normalising the epidemic within the community could go some way to allaying the fears shrouding testing, if such services are designed with the specific needs of youth in mind. This paper adds to the body of literature informing the design of policy in South Africa aimed at integrating HCT into school health services.