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Sub-Saharan Africa holds 90% of the HIV-infected children worldwide and most of them are infected through vertical transmission. This project set out to assess the extent of clinic-level PMTCT prophylaxis coverage in the resource-limited setting of the Free State province, in South Africa. Adherence to treatment during the single-dose nevirapine regimen for HIV-positive pregnant women, as well as accuracy of clinic records so as to inform better service implementation were measured. A total of 1572 mother-infant pairs were included in a cross-sectional survey carried out in rural antenatal and delivery services from two health districts between 2007 and 2008. In the findings, the clinic records under-estimated maternal HIV prevalence in mothers. Also,19.4% of the HIV positive women recorded to have been offered nevirapine during labor, did not actually ingest it. The more frequently a woman sought antenatal care during pregnancy, the more likely she was to ingest nevirapine. Women who had at least 4 antenatal visits were 4.5 times more likely to adhere than women who attended services only once. Interventions are needed to improve antenatal care uptake and routine data quality.