HIV infection is associated with an increased prevalence of common mental disorders and with the development of HIV associated neurological disorders (HAND). The aim of this research was to determine the reliability of lay adherence counsellors in the administration of the substance abuse and mental illness symptom screener (SAMISS) for common mental disorders and International HIV Dementia Scale (IHDS) for HAND in a South African sample of 269 people living with HIV/AIDS and on HAART in a primary healthcare setting. We used a cross-sectional design with each patient assessed by a mental health nurse and counsellor, 1 week apart. Reliability was fair for the SAMISS overall (κ = 0.39, CI(95) 0.29-0.49, P < 0.01), but was higher for the substance abuse component compared to the mental illness component. Reliability for the IHDS between counsellors and nurses was slight (κ = 0.11, CI(95) 0.00-0.27, P < 0.02). Counsellors tended not to miss symptoms, and detected symptoms more often than nurses for the both the SAMISS and IHDS. Strategies to improve the ability of primary healthcare providers to screen for neurocognitive disorders as well as avoiding over-detection of mental illness and substance abuse symptoms need to be developed and implemented for the primary healthcare setting.