Recent WHO/ILO/UNAIDS guidelines recommend priority access to HIV services for health care workers (HCWs), in order to retain and support HCWs, especially those at risk of occupationally acquired tuberculosis (TB). The purpose of this study was to identify barriers to uptake of HIV counselling and testing (HCT) services for HCWs receiving HCT within occupational health units (OHUs). Questions were included within a larger occupational health survey of a 20% quota sample of HCWs from three public hospitals in Free State Province, South Africa. Of the 978 respondents, nearly 65% believed that their co-workers would not want to know their HIV status. Barriers to accessing HCT at the OHU included ambiguity over whether antiretroviral treatment was available at the OHU (only 51.1% knew), or whether TB treatment was available (55.5% knew). Nearly 40% of respondents perceived that stigma as a barrier. When controlling for age and race, the odds of perceiving HIV stigma in the workplace among patient-care health care workers (PCHWs) were 2.4 times that for non-PCHWs [95% confidence interval (CI): 1.80-3.15]. Of the 692 survey respondents who indicated a reason for not using HIV services at the OHU, 38.9% felt that confidentiality was the reason cited. Among PCHWs, the adjusted odds of expressing concern that confidentiality may not be maintained in the OHU were 2.4 times (95% CI: 1.8-3.2) that of non-PCHWs and were higher among Black [odds ratio (OR): 2.7, CI: 1.7-4.2] and Coloured HCWs (OR: 3.0, 95% CI: 1.6-5.6) as compared to White HCWs, suggesting that stigma and confidentiality concerns are still barriers to uptake of HCT. Campaigns to improve awareness of HCT and TB services offered in the OHUs, address stigma and ensure that the workforce is aware of the confidentiality provisions that are in place are warranted.