The resurgence of the polio virus in Nigeria following vaccine rejections poses a severe threat to the total worldwide eradication of polio. Vaccine refusals are a huge problem in Nigeria, especially in the North, which accounts for about 60 percent of polio cases in 2013. These refusals were informed by claims that polio vaccines contained anti-fertility properties that were designed by the ‘West’ to reduce the Muslim population. These claims and subsequent vaccine rejections culminated in the killing of health workers during an immunisation exercise in February 2013. This study is an analysis of the coverage of the polio eradication controversy by two newspapers- Punch and Daily Trust, following the killings of the health workers. Daily Trust is situated in Northern Nigeria, while Punch is situated in the South. The choice of these newspapers is based on the argument by Ayodele (1988) and Omenugha (2004) that the Nigerian press has been accused of escalating tension in the country because they view many aspects of the Nigerian reality from the lenses of religious, political and cultural prejudices. Because it is a text-based study, the chosen research method is Fairclough’s (1995) model of Critical Discourse Analysis (CDA), following a preliminary thematic content analysis. In addition to Fairclough’s model, the study employs textual analytic tools such as narrative analysis and rhetoric/argumentative analysis. The selected texts, which comprise editorials and news stories are analysed based on the themes identified during the thematic content analysis. The study concludes that while the two newspapers differ in their locations and stylistic approach to news, they are similar in their coverage of the polio eradication crisis. They both side with the Federal Government and help perpetuate the South versus North animosity thereby ignoring the intricacies involved in the polio eradication controversy.