Health provision in South Africa requires a focus on primary health care within the public health system. Medical practitioners continue to migrate from the public health service. Given the need for human resources in primary health care, this study was conducted to explore the perceptions and experiences of newly-qualified medical practitioners (interns) about pursuing a career in primary health care in the public health sector. This exploratory, qualitative study specifically explored the factors related to interns' perceptions about careers in primary health and child health care in the public health service in five hospitals in KwaZulu-Natal (KZN). Data was collected through focus group discussions with a purposive sample of intern participants, who were chosen for having had the necessary experience to decide on long-term careers. The data were coded, categorised and themed using a combination of manual and computer-assisted methods. (NVivo 11 software). Themes both external and specific to the intern-supervisor relationship were identified that influences intern career intentions. A high disease burden in resource-constrained institutions that are perceived to be poorly managed and sub-optimal intern-supervisor relationships lead to inadequate participation within 'communities of practice' during internship. Interns viewed careers related to primary health care negatively, preferring to specialise in other fields. Multiple challenges are identified when participating in caring for adults and children in KZN's public health service. This coupled with a perceived inadequate supervisor support favour interns to see medical specialisation as a more feasible career option rather than primary health care. Experiences during internship possibly influence future career intentions that are discordant with SA's national health priorities. Improving the intern working environment may be a way forward to stimulate interns' interests in careers congruent with SA's health needs, specifically careers in primary health care.