BACKGROUND: There is widespread agreement that civil war obstructs efforts to eradicate polio. It is suggested that Islamist insurgents have a particularly negative effect on vaccination programmes, but this claim is controversial. METHODS: We analyse cross-national data for the period 2003-14 using negative binomial regressions to investigate the relationship between Islamist and non-Islamist insurgency and the global distribution of polio. The dependent variable is the annual number of polio cases in a country according to the WHO. Insurgency is operationalized as armed conflict between the state and an insurgent organization resulting in ≥25 battle deaths per year according to the Uppsala Conflict Data Programme. Insurgencies are divided into Islamist and non-Islamist insurgencies. We control for other possible explanatory variables. RESULTS: Islamist insurgency did not have a significant positive relationship with polio throughout the whole period. But in the past few years - since the assassination of Osama bin Laden in 2011- Islamist insurgency has had a strong effect on where polio cases occur. The evidence for a relationship between non-Islamist insurgency and polio is less compelling and where there is a relationship it is either spurious or driven by ecological fallacy. CONCLUSIONS: Only particular forms of internal armed conflict - those prosecuted by Islamist insurgents - explain the current global distribution of polio. The variation over time in the relationship between Islamist insurgency and polio suggests that Islamist insurgent's hostility to polio vaccinations programmes is not the result of their theology, as the core tenets of Islam have not changed over the period of the study. Rather, our analysis indicates that it is a plausibly a reaction to the counterinsurgency strategies used against Islamist insurgents. The assassination of Osama bin Laden and the use of drone strikes seemingly vindicated Islamist insurgents' suspicions that immunization drives are a cover for espionage activities.