Background The public health consequences of the Iraq War (2003–2011) have remained difficult to quantify, mainly due to a scarcity of adequate data. This paper is the first to assess whether and to what extent the war affected neonatal polio immunisation coverage.

Method The study relies on retrospective neonatal polio vaccination histories from the 2000, 2006 and 2011 Iraq Multiple Indicator Cluster Surveys (N=64 141). Pooling these surveys makes it possible to reconstruct yearly trends in immunisation coverage from 1996 to 2010. The impact of the war is identified with a difference-in-difference approach contrasting immunisation trends in the autonomous Kurdish provinces, which remained relatively safe during the war, with trends in the central and southern provinces, where violence and disruption were pervasive.

Results After controlling for individual and household characteristics, year of birth and province of residence, children exposed to the war were found to be 21.5 percentage points (95% CI −0.341 to −0.089) less likely to have received neonatal polio immunisation compared with non-exposed children.

Conclusions The decline in neonatal polio immunisation coverage is part of a broader war-induced deterioration of routine maternal and newborn health services. Postwar strategies to promote institutional deliveries and ensure adequate vaccine availability in primary health facilities could increase dramatically the percentage of newborns immunised.