BACKGROUND: For people living with HIV (PLWH), the burden of travelling to a clinic outside of one's home community in order to reduce the level of stigma experienced, may impact adherence to treatment and accelerate disease progression. METHODS: This study is set in the Agincourt Health and Demographic Surveillance System (HDSS) in South Africa. Probabilistic and interactive methods were used to individually link HDSS data with medical records. A regression analysis was used to assess whether travel distance was correlated with the condition for which individuals were seeking care (primarily HIV, diabetes or hypertension). For PLWH, a Cox proportional hazard regression model was used to test for an association between the distance travelled to the clinic and late attendance at follow-up visits. RESULTS: The adjusted relative risk (RR) of travelling to a clinic more than 5 km from that nearest to their home for HIV patients compared to those being treated for other conditions was 2.78 (95% confidence interval (CI) = 2.23-3.48). The adjusted Cox regression model showed no evidence for an association between the distance travelled to a clinic and the rate of late visits. (RR = 1.00, 95% CI = 0.99-1.00). CONCLUSIONS: The findings were consistent with the hypothesis that people living with HIV/AIDS would be willing to accept the burden of increased clinic travel distances in order to maintain anonymity and so limit their exposure to stigma from fellow community members. For those seeking HIV care the lack of an association between increased travel distances and late visit attendance suggests this may not impact treatment outcomes.