BACKGROUND: In South Africa the ever increasing demand for antiretroviral treatment (ART) runs the risk of leading to sub-optimal care in public sector ART clinics that are overburdened and under resourced. This study assessed the quality of ART services to identify service areas that require improvement. METHODS: A cross-sectional study was carried out at 16 of 17 public ART clinics in the target area in greater Pretoria, South Africa. Trained participant observers presented as ART qualifying HIV positive patients that required a visit to assess treatment readiness. They evaluated each facility on five different occasions between June and November 2009, assessing the time it took to get an appointment, the services available and accessed, service quality and the duration of the visit. Services (reception area, clinician's consultation, HIV counselling, pharmacy, nutrition counselling and social worker's assessment) were assessed against performance standards that apply to all clinics. Service quality was expressed as scores for clinic performance (CPS) and service performance (SPS), defined as the percentage of performance standards met per clinic and service area. RESULTS: In most of the clinics (62.5%) participant observers were able to obtain an appointment within one week, although on the day of their visit essential services could not always be accessed. The median CPS of the assessed facilities was 68.5 with four clinics not meeting minimum standards (CPS > 60). The service areas that performed least well were the clinician's consultation (SPS 67.3) and HIV counselling (SPS 70.7). Most notably, clinicians performed a physical examination in only 41.1% of the visits and rarely did a complete TB symptom screening. Counsellors frequently failed to address prevention of HIV transmission. CONCLUSIONS: Overall public sector ART clinics in greater Pretoria were easily accessible and their services were of an acceptable quality. However, the time spent at the clinic to complete the services was found to be very long and there was considerable variation in adherence to performance standards within the services, particularly in respect of clinician's consultation and counselling. Clinic management needs to ensure efficient clinic organisation and to improve adherence to performance standards in key service areas.