BackgroundThe news media is located at the nexus of the public and policy agendas and provides a window into issues concerning the public. Therefore, it could be a powerful tool for advocating for citizens’ health and could help promote evidence-based primary health systems responsive to the needs of citizens. However, research on the coverage of primary healthcare and related research evidence in the South African print media is virtually non-existent.MethodsWe examined 2,077 news stories that covered primary healthcare from 25 South African newspapers retrieved from the Lexis-Nexis online archive over a 16-year period (1997–2012). We analysed basic characteristics and conducted a content analysis of the news stories.ResultsOf the 2,077 news stories that mentioned primary healthcare, this was the main focus in 8.3% (n = 173). Of these, 45.7% discussed issues relating to clinics, whereas issues relating to community health workers and nurses were covered by 42.8% and 34.1% of news stories, respectively. The number of news stories discussing infectious diseases (55.5%) was more than twice the number discussing non-communicable diseases (21.4%). HIV/AIDS/TB illness- and service-related issues were covered by 54.3% of news stories and social determinants of health by 22%. Issues relating to how healthcare is organised to deliver services to the people received substantial coverage in the print media, with 72.8% discussing delivery arrangements, 72.3% governance arrangements, and 55% financial arrangements. A small fraction of news stories (7.5%) discussed research studies but none discussed a systematic review.ConclusionOur study underscores the potential role of media analyses in illuminating patterns in print media coverage of health issues. It also shows that an understanding of coverage of health research evidence could help spur efforts to support the climate for evidence-informed health policymaking. Researchers in low- and middle-income countries need to be more proactive in making use of media analyses to help illuminate health related issues that require the attention of health policymakers, stakeholders and reporters, and to identify potential areas of research.Electronic supplementary materialThe online version of this article (doi:10.1186/s12961-015-0051-6) contains supplementary material, which is available to authorized users.