For over 50 years, concerns have been raised about the risk of pertussis vaccine-induced childhood encephalopathy and epilepsy. This article reviews the scientific literature, and the social and historical context in which the scientific, public health and societal views have not always been aligned. Large-scale studies of this issue have produced conflicting results, although the recent consensus is that the risk of vaccine-induced encephalopathy and/or epilepsy, if it exists at all, is extremely low. Risk estimates in the literature have included: risk of a febrile seizure 1 per 19,496 vaccinations; risk of an afebrile seizure 1 per 76,133 vaccinations; risk of encephalopathy after pertussis infection nil-3 cases per million vaccinations. A recent study showed that encephalopathy in 11 out of the 14 children studied, although previously attributed to vaccination, was in fact due an inherited genetic defect of the SCNIA gene that codes for the voltage gated neuronal sodium channel. This study is important because it provides a solid alternative explanation for the perceived pertussis vaccine-encephalopathy association. The interesting possibility is raised that the encephalopathy apparently due to pertussis itself may, in some cases, be due to an SCNIA mutation. It may also, by analogy, shed some light on the continuing debate about other serious long-term adverse effects of vaccination in general.