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► We identified 2608 narcolepsy cases in 6 EU countries between 2000 and 2010. ► After pandemic vaccination, incidence rates increased in Finland, Sweden and Denmark. ► In Denmark, the increase did not follow high pandemic vaccination coverage. ► In Italy, the Netherlands and the United Kingdom no increased rates were seen. In August 2010 reports of a possible association between exposure to AS03 adjuvanted pandemic A(H1N1)pdm09 vaccine and occurrence of narcolepsy in children and adolescents emerged in Sweden and Finland. In response to this signal, the background rates of narcolepsy in Europe were assessed to rapidly provide information for signal verification. We used a dynamic retrospective cohort study to assess the narcolepsy diagnosis rates during the period 2000–2010 using large linked automated health care databases in six countries: Denmark, Finland, Italy, the Netherlands, Sweden and the United Kingdom. Overall, 2608 narcolepsy cases were identified in almost 280 million person years (PY) of follow up. The pooled incidence rate was 0.93 (95% CI: 0. 90–0.97) per 100,000 PY. There were peaks between 15 and 30 year of age (women>men) and around 60 years of age. In the age group 5–19 years olds rates were increased after the start of pandemic vaccination compared to the period before the start of campaigns, with rate ratios (RR) of 1.9 (95% CI: 1.1–3.1) in Denmark, 6.4 (95% CI: 4.2–9.7) in Finland and 7.5 (95% CI: 5.2–10.7) in Sweden. Cases verification in the Netherlands had a significant effect on the pattern of incidence over time. The results of this incidence study provided useful information for signal verification on a population level. The safety signal of increased narcolepsy diagnoses following the start of the pandemic vaccination campaign as observed in Sweden and Finland could be observed with this approach. An increase in narcolepsy diagnoses was not observed in other countries, where vaccination coverage was low in the affected age group, or did not follow influenza A(H1N1)pdm09 vaccination. Patient level analyses in these countries are being conducted to verify the signal in more detail.