AIM: To identify factors that influence adherence to antiretroviral (ARV) prophylaxis by HIV positive mothers participating in the HIV prevention of mother to child (PMTCT) programme. METHODS: Post-delivery 815 HIV-infected mothers aged 18 years and above with babies aged 3-6 months were interviewed in Gert Sibande District, Mpumalanga province, South Africa. RESULTS: Eighty five percent of the mothers indicated that they had been provided with nevirapine and 78.4% took it before or at the onset of labour and infant nevirapine intake was 76.9%. In multivariate analysis it was found that women with better PMTCT knowledge had a higher perceived confidentiality about HIV status at the health facility. They had a term delivery and those who had told their partner about nevirapine had a higher maternal nevirapine adherence. Women who had also told their partner about nevirapine, whose partner was asked for an HIV test and those who knew the HIV status of their infant had higher infant nevirapine adherence. CONCLUSION: Adherence to maternal and infant ARV prophylaxis was found to be sub-optimal. Health services delivery factors, male involvement, communication and social support contribute to adherence to ARV prophylaxis in this largely rural setting in South Africa.